Q: Decrypting a 3ds/cia file

I used [Batch CIA 3DS Decryptor] and it seems to work fine. But I have three question about it.
Q1: When I decrypt a 3ds/cia file, the outputted file is not always the same. Meaning that if I do the following:
1- Decrypt the file {Game.3ds} and it gives me the file {Game-decrypted.3ds}
2- Move {Game-decrypted.3ds} to another place (desktop)
3- Decrypt the file {Game.3ds} again and it gives me the second {Game-decrypted.3ds}
The hashes (MD5) for the two outputted files are not the same. Why? is the process somehow different each time I use the program?
Q2: Is there a way to disable the trimming feature. Just in case I want to use another program to trim like (NDSTokyoTrim 3.1) or don’t want to trim at all?
Q3: Is there a way to reverse the process (getting the encrypted files back, with the original hash) ?If it is impossible with this tool (or after the use of this tool), then is there a way to decrypt 3ds/cia files that is reversible?
*I use the tool for decrypting my files for emulation with Citra.
*I didn’t decrypt the already decrypted files again, but I decrypted the original file twice to check if it gives me different results, which it did (MD5 mismatch). Also, I did check if the original file was changed after the first decryption, and it wasn’t (MD5 match).
So, this tool seems to give slightly different results when applied on the same file. The inconsistency is surprising (and maybe unreliable), which made me ask Q1.
*I want the ability to return my decrypted files to their original encrypted form (MD5 perfect) for archival purposes, which made me ask Q2, Q3

Note: I’m a noob .So, if there are Windows tools (so I don’t brick my 3DS) or ways to do this (or some step by step explanation) it would be appreciated. If there isn’t, then go ahead and hit me hard with what you have.