You, as the DM, can practically create any template you wish. Your imagination should not be limited by the published rules. Of course, you should pay attention to game balance and such stuff (unless you're feeling quite nasty and your players tolerate your being so. :))
In fact, you can easily improvise creatures on the fly as well. (At least I often do that when running DnD - and my players don't seem to mind. They're in for the story. :)) However, if you feel safer designing your monsters and monster templates in advance, there are resources that may help, such as this official 3.5 article at wizards.com.
As for a more specific answer: I'd say sure, use other dragons for the half dragon template, but pay attention to game balance and world building issues (see the article linked above) when modifying/redesigning the template to suit both your needs and your preferred other dragon (or dragon-like creature.) Know that in fact you won't be using the official half-dragon template but a customized, "house-rules" version of it - not as if there was anything wrong with that. :)
Time travel to the past instantaneously then time travel to the future conventionally
A magic portal can be created that transports its users to the past (and only to the past). Such a portal is created by a caster using the 9th-level Sor/Wiz spell teleport through time [conj] (Perilous Gateways Web column "Portals in Time: The Portal through Time (Part 2)") and the epic feat Create Time Portal (Perilous Gateways Web column "Portals in Time: The Portal through Time (Part 3)). The black dragon could travel through a portal that's created to send users 100 years into the past then just wait.
Conceivably, the portal is unnecessary: the black dragon could simply pay a sorcerer or wizard to cast the spell teleport through time on the dragon's behalf and have them both sent 100 years into the past, but such a spellcasting service is beyond what can normally be purchased, costing, as it does, at least 6,530 gp, over twice what a generally available spell can cost. Further, demographics limit the availability of such a caster as does self-preservation: such a caster must be as willing as the black dragon to travel to the past, after all. (Some oddball casters might not care, though. Also, the spell doesn't allow travel to the future, either.)
Thus the high cost of the spell teleport through time and the difficulty of gathering its wacky material component make the time portal a more reasonable choice than, for example, an adventurous, accommodating lich. Note that such a portal needn't be created for this purpose: it could've been created to transport users to that time a year ago by a contemporary historian or 90 years ago by a madman desperate to relive the last few years with his departed pet or whatever. (A madman because this is dangerous considering the consequences of meeting oneself as the articles describe.)
Create a flowing time trait demiplane
It's the DM's call whether the 9th-level Sor/Wiz spell genesis [conj] (Epic Level Handbook 117) allows the creation of demiplanes with the caster's choice of the trait flowing time. But if the DM allows the spell to create such a demiplane, a creature as low as level 13 can create such a demiplane. A wyrmling black dragon will likely have to wait until it's at least juvenile to have treasure sufficient to do this, but maybe it can get a loan, ask its parents for aid, sell its soul, or somehow rustle up power asymmetrically another way.
Are you okay with Dragonlance?
The Dragonlance campaign setting includes the feat Create Skull Totem (Age of Mortals 209). Although not published by Wizards of the Coast like the Dragonlance Campaign Setting, Age of Mortals nonetheless is officially licensed by Wizards of the Coast, bearing a seal saying so and everything. Anyway. The feat Create Skull Totem has as prerequisites the feat Draconic Vampirism (Dragons of Krynn 168-9) (also licensed) and being a spellcaster. When it has the feat, the dragon goes around serial killing other dragons for their fresh skulls and, when it has enough of the right kinds of dragon skulls, it can switch on the totem and start gaining virtual age categories, the text saying each virtual age category is "as if [the dragon] had gained an actual age category beyond its current one" (209). So, a level of wizard, a couple of obscure feats, a bunch of dead dragons, and—poof!—instant threat to the campaign's status quo.
Although it's way cooler to have a vampiric dragon build a magic pyramid out of dragon skulls, also in Dragonlance there's the 8th-level Sor/Wiz spell hasten the end [necro] (Holy Orders of the Stars 70) (still licensed). The spell allows the caster to concentrate for as long as the caster wants to age a creature by 10 years each round, but each round the creature also gains a negative level, and negative levels equal to Hit Dice are fatal. So having a necromancer cast hasten the end on the dragon requires the dragon to trust that necromancer a lot, but, if all goes well, a couple of hasten the end and greater restoration spells later, and the wyrmling should be big enough to be the threat he wasn't before.
Best Answer
There's no specific prohibition against applying the half-dragon template to a dragon.
However, applying templates to monsters is DM business. It's not something that will happen just randomly out of nowhere, or by a player's initiation — templates are tools, and most exist only to get a job done as needed by a DM. A DM who needs to make a half-dragon dragon has the template available to do so, and presumably has an excellent reason for such a strange operation. However, it can be expected that most DMs will never have need for such a combination, and as such the combination will never appear in majority of real games.
The game is, in many ways, stupid. A stupid tool is an obedient and flexible tool. In such matters it doesn't try to be smarter than the people who use it, leaving such discrimination up to the DM's intelligent choices regarding a given campaign's needs.