EvoCRC is always compressing and storing files to the "clean ROM" folder.
it's for archival purpose, not for renaming games on SD.
Sorry that it started to pack them on your SD
I didn't know you wanted to renamed the ROM you were actually playing.
Users asked the feature to not compress files.
Maybe it will be added on a later version. the new developer is listening to user's request and update it a lot.
If you only want to rename the .3ds or .3dz file, maybe you can download the .dat file from EvoCRC, and use OfflineList to rename the games. I think It's possible to rename without zipping.
Or maybe someone should create a renamer (not a repacker).
The "Rebuild archive" option is used to extract the contend of already created archives if the content doesn't match the option you chose to include (cover, nfo, etc.), then rebuild it with the correct content and the correct compression ratio.