Does encrypting different versions of the same file or folder with the same key make it easier for hackers to attempt the decoding? Assuming the hacker has access to the ciphers of each of the versions, will it help him/her to decipher the original file(s) by doing some sort of comparison of the ciphers?
For modern ciphers when well-implemented, no: encrypting different versions of the same plaintext(s) with the same key does not make the cipher attackable.

That's because adversaries having access to nearly the same data encrypted multiple times is part of what's assumed in the baseline attack model for all modern ciphers: Choosen Plaintext Attack. The cipher is nearly never the weak link in the security chain. That's true including for AES-CTR.

Problems do occur when the random generator used for the Initialization Vector fails, or is omitted; indeed CTR mode is sensitive to that.

To a lesser degree, some side-channel attacks could be facilitated by multiple slightly different plaintexts.