So... I added various sources to my add-paths and I have only one romset to be fixed.
Added destination (/destination/path/to/fixed/roms), OK.
Database created, OK.
Added other add-paths, Ok.
Settings > Merge mode > split is for all: split-rom, split-bios, split-samples (samples has correct directory defined: /destination/path/to/fixed/seamples).
Settings > Operations > I select all, but not "Remove zip comments".
Settings > Fix options > Corrupted files > "Don't touch".
Settings > Case > ignore-files and ignore-roms ; Various > zip compression
After 16 hours of fixing and only 72 files updates, I still have no CHDs subfolders, neither samples added to their destination ...
Please help, thanks!