I previously noted the usual idea about how the word synderesis came about: that it was originally syneidesis, and that St. Jerome in his commentary on Ezekiel probably wrote it that way, particularly given that he seems to translate it fairly directly into Latin as conscientia. St. Thomas, however, for philosophical reasons distinguishes synderesis and conscientia, while recognizing that many people don't make a distinction.
However, Sarah Byers has an interesting argument for an alternative view. Her idea is that the original word was actually sunteresis, and synderesis is just an ordinary medieval Latin spelling variant for that. Sunteresis means something like 'safeguarding, protecting, taking care of'. It's not a common version of the Greek word, which is why it's usually not regarded, although the shorter teresis is not too difficult to find. Byers argues, however, that St. Jerome is probably influenced by Origen on this point; we don't have Origen's commentary on Ezekiel, but the fragments we have suggest that he might have made use of Stoic vocabulary, in which sunteresis and its variants are sometimes found. This is fairly tenuous -- although it seems possible -- but if this is the case, then it would mean that St. Thomas's distinction between synderesis and conscientia (synedeisis) might be a return to an older distinction that was lost in other texts. Very interesting, and worth at least considering: synderesis as the natural safeguard or caretaker for the human being and human conscience.