A recent question asks whether the modifier "clearly" changes the meaning of "evident". I would have said, prior to examining a few dictionaries, that evident did not necessarily mean readily apparent, but to my surprise it does.
This brings me to ask what word or expression would mean something can be taken as a true fact, but not through an easily constructed (not obvious or readily apparent) rationale?
For example, if Sherlock Holmes says something is true while everyone else is still sitting on their hands, then it is evident to Holmes, but not to the rest of the world. So, from everyone else's point of view, it is not readily apparent, and (by definition) apparently it is not evident, clear, or clearly evident at all, based on the dictionary definitions. But (let's stipulate) it is true and deducible from the observable evidence. What would we call this?
Update
An update is highlighted above. I can see from some of the answers and comments that I may have gone off my mark with the phrase "not through an easy-to-follow rationale”, and I have modified the question to correct this. I understand that there can be rationales, arguments, or proofs that, once explained, may or may not be easy to follow. What I intend is that the rationale to support the indisputable conclusion is not (initially) easy to recognize or construct (not readily apparent) in the first place. I apologize for the confusion. (The original can be seen in the change history.)
Update 2
Shortly after offering a bounty to this request, I recalled a single word that I now believe is a very good match to the parameters specified in this inquiry as it is stated above. That word has not yet been suggested (or approached) by any answer or comment (active or deleted) at the time of this edit. This request is changed to a single word request. (However, if you feel a single word fits well but not without some additional supporting words, please offer your thoughts in an answer.) While my curiosity for the term has already been met, the request and bounty remain as an open challenge. I will post my own answer once the bounty has expired and been awarded.
Best Answer
One word that comes to mind is "provable" or "scientifically provable" with the connotation of proof such as used in sciences like geometry or philosophy. The method that Sherlock Holmes used was based on how scientific proofs are built. There are many things which science has proven which, at least at one point of time, were not evident to many people. Even today, I'm sure a vast number of people do not find the principals of calculus evident, although they are certainly provable.
In philosophical terms you can prove something using a posteri knowledge or a priori knowledge. A posteri knowledge relies on empirical evidence, though it may be subject to false results especially with limited observations (if you flip a coin 3 times and the coin turns up heads all 3 times that doesn't mean it will always be heads, for instance). However, given enough observations, something proven a posteri can be quite evident to anyone aware of the many observations.
On the other hand, something proven a priori may not be evident to many people even when they are fully aware of the logic of the a priori finding. For instance, when the concept that "all men are created equal" was put forth as an a priori finding, despite the detail of the support, it remained non-evident to many people, so I'll also submit (complex) "a priori knowledge" as something that includes many things that are not necessary evident but are considered true. To be more specific, I mean non-definitional a priori knowledge since most definitions are considered a priori knowledge and are usually generally accepted as evident to all. "Red is a color" is a priori but also, in my opinion, evident based on the accepted definition of "color". So I don't mean simple definitional a priori knowledge. I'm referring more to more complex a priori knowledge such as "everyone has a right to freedom."
I think it's important to mention both "provable" and "complex, non-definitional a priori knowledge" because together these cover, I believe, the whole range of what could be considered, at least by some people, true but not evident to many other people. The Sherlock Holmes method using scientific proofs would not capture the whole range of a priori knowledge because this knowlege is generally not of the type that can be known to a scientific certainty, and Holmes builds on things that are more provable using a posteri knowledge. On the other hand, I couldn't only mention a priori knowledge because there are many things which are scientifically provable but of a very complex nature so these remain non-evident to many people simply because of their complexity. So many provable things which are a posteri are also part of this answer.
EDIT: After seeing the answer that received the bounty and some of the comments from the questioner, I am disappointed, to say the least. The ultimate bounty was awarded to cryptic. However, the question required that the non-apparent thing also be a true fact and words like cryptic do not take any position on whether something is true or not. Something can be cryptic and true just as likely as it can be cryptic and not true. So to use cryptic would not convey that something is a true fact. I offer the following:
Even in the answer provided for cryptic which included the definition, no part of that definition or answer claimed that cryptic means something true or a fact.
Cryptic is often a word associated with the occult which I think most people believe has connotation which is the opposite of truth: the primary definition from dictionary.com is "hidden; secret; occult". Cryptic is also a word associated with Masonic organizations. This website published by the Grand Council of Cryptic Masons talks about the Cryptic Rite which it says is part of "a Masonic allegory. Freemasonry is very philosophical and teaches its ideals by allegory or story." Obviously an allegory is not a true fact, but it can be cryptic. http://www.yorkriteofcalifornia.org/council/whatis.html
Cryptic is often applied to emotions and behavior and lots of other things which are not true facts. Poet Edward Arlington Robinson once wrote, "With a cryptic idiotic melancholy" to describe the observed emotions of some birds. One rarely uses idiotic to describe something one believes to be a true fact. Similarly Victor Marie Hugo in "Notre Dame de Paris" wrote "This is the second transformation of architecture—no longer cryptic, sacerdotal, inevitable, but artistic, progressive, popular—beginning with the return from the Crusades and ending with Louis XI." Here cryptic is simply implying that the older style was less accessible, not that it was more true than the later style.
Cryptic is often used when the truth of something is unknown. For instance the Voynich Manuscript is often described as cryptic but people have no idea if it's authentic or a hoax, though most seem to lean towards it likely being a cryptic hoax.
Similes for cryptic which the questioner also liked, such as obscure (his second choice per his comment), suffer from the same problems in that they give not indication that something is a true fact. Their definitions do not state that they mean something true or something which is a fact. They are often applied to emotions and behavior and many other things which are not true facts. They can be, and often are, applied to things where the trueness of the thing is currently unknown. One recent tripadvisor comment warned of "false advertising and obscure location" which has the connotation of a location which is deceptively difficult to reach for the unwary traveler. If I refer to an "obscure religion" I don't mean I believe it is the one, true religion.
So summing up a long rant, I'm hugely disappointed because the questioner asked for a word or phrase that also meant a true fact and then ignored that extremely difficult and challenging requirement in selecting the bounty winner.