I commented on it, but linking it here for quickness
Just delete the folder fix the issue, hope it break nothing ahah, thanks for the help !
Hi, an upgrade is regarded as a module and SuiteCRM maintains a copy of every file which is replaced as a restore for the case where you would want to uninstall a module, which doesn't make sense for upgrades.
The proper solution would be for SuiteCRM not to create restore files for modules that have the following property in the manifest:
'is_uninstallable' => false,
Deleting files from the module loader is only possible once they are first uninstalled which is not possible for upgrades. The delete function then deletes the installer package, not the restore files (which for uninstallable modules would have been restored by uninstalling the module).
For now you would delete these files manually after upgrading.