Migrate to a different server with different paths

Initially was running Ubooquity in my QNAP but I'm trying to have it in a dedicated server with more memory and CPU power.

The issue I'm facing is that in the new Server the paths are different so as soon as I start Ubooquity (tar from the QNAP NAS) is deleting all the comics.

Is there a way to change the path before Ubooquity runs a scan and deletes all the comics?

I could create symlinks to replicate the original paths but I think Ubooquity has issues with simlinks.

Any help will be appreciated. Thanks.