The description of the encode thoughts cantrip says (GGtR, p. 47; emphasis mine):
Putting a finger to your head, you pull a memory, an idea, or a
message from your mind and transform it into a tangible string of
glowing energy called a thought strand, which persists for the
duration or until you cast this spell again. […]If you cast this spell while concentrating on a spell or an ability
that allows you to read or manipulate the thoughts of others (such as
detect thoughts or modify memory), you can transform the thoughts or
memories you read, rather than your own, into a thought strand. […]Casting this spell while holding a thought strand allows you to
instantly receive whatever memory, idea, or message the thought strand
contains. […]
It seems that it is intended that the memory is removed. This could, perhaps, create an unintended, strong combo with detect thoughts and obsolesce the modify memory spell.
It also could be more reasonable in scope of power for encode thoughts to simply render a copy of the thought, though this doesn't seem to be what the spell says it does.
Does encode thoughts remove the targeted thought from the creature's memory, or does it create a copy of that thought?
Related and inspired by: Can a creature with a Mind Blank spell active on itself target itself with Encode Thoughts?
Best Answer
Encode thoughts does not modify memories
As you say, the phrase "pull from" can mean removing something from its place, and usually this is exactly what is meant when referring to physical objects. For example: "The dentist pulled the patient's tooth from his mouth."
However, when used with things that are easily reproduced, such as thoughts or computer data, "pull from" almost always implies making a copy. For example: "The wizard was able to solve her mystery by pulling from the vast archives of knowledge in the library." No one would read this sentence and assume that the wizard was running around the library literally pulling pages out of books.1 It's so unambiguous that you wouldn't even think to ask for clarification.
The situation is the same with the text in the encode thoughts spell: a thought is not a physical object and is easily reproduced, so the clear intent is that the spell creates a copy of the thought without removing or modifying the original.
If the spell modified your memories, it would say so explicitly
Consider the text of the modify memory spell. It spends 3 entire paragraphs describing the process of modifying the target's memory, and the consequences thereof, in exacting detail. This is good, because figuring out how to role play false memories is difficult, and you need all the guidance you can get. In contrast, there is no text describing any memory-modifying effects in encode thoughts. The closest thing is the use of the phrase "pull from", which by itself is not sufficient to imply that a lowly cantrip can produce such a powerful effect as memory modification.
Further evidence
There are additional details that make it even clearer that copying thoughts, not removing, is the intended interpretation.
Having the spell remove the thought would be either pointless or overpowered
While holding a thought strand, you can cast Encode Thoughts to read the thought stored in it. Since the spell is a cantrip, you can cast it as many times as you like. So, even if the spell did remove the thought from the caster's mind, they could just cast it again to read the thought back into their mind. So the initial removal of the thought would be pointless in this case. Furthermore, the use of the spell to read a thought from a thought strand is unambiguously a "copy" operation, so it would be weirdly asymmetric if the reverse operation was not.
Alternatively, if the combination of Encode Thoughts with Detect Thoughts could remove a thought from someone else's mind, that would be obviously overpowered. This would allow memory modification with no saving throw using a 2nd level spell, which is clearly overpowered given that Modify Memory is a 5th level spell, and spells that can negatively affect other creatures are rare and almost always high level (e.g. the various Power Word spells).
Encode Thoughts is a secret communication channel
As explained in Guildmaster's Guide to Ravnica, House Dimir is a secretive organization that uses thought strands as a secret means of communication:
Hence, the intended use of the spell is similar to Thieves' Cant and Druidic: a secret communication channel available only to those with the specific knowledge required to access it. In this context, having the spell remove memories instead of copying them doesn't make a lot of sense.
1Although if the wizard is a servant of Vecna, all bets are off.