Cannot uninstall External Entities Files

I'll check that once I'm done with the translation support issue.
It's weird though. I don't see how the system would know about external files since their virtual file identifier is not in the database.

First, I'd like to clarify one thing: from my perspective, you cannot use External Entities 3.0.0 with the xnttfiles module as they are not compatible. The "xnttfiles" module is compatible with external entity 2.0.x and has been integrated into 3.0.0 core now.

The problem you are referring to, however, is reproducible in 3.0.0 using the "External entities file and image fields support" sub-module.
I can reproduce the problem and I'll fix for v3. If you really have xnttfiles module installed, it might probably be because you updated from 2.0.0 to 3.0.0. I got a dev site with both xntt 3.0.0 and xnttfiles, so it is not impossible but it should not happen on clean installs.

Could you confirm which version of External Entity module you're running (2.0.x or 3.0.x) and if you are really using the xnttfiles → module (while a 3.0.0 update should have replaced the use of the xnttfiles module by the xntt 3.0.0 core file features).

UPDATE: It needs more than a simple fix. An "external file storage" class needs to be created to replace all the default file storage class methods that relies on database entries. I've started some work and it will be fixed for v3. I hesitated to change the priority to "Major" as it should be uninstallable without any issue but it does not prevent the system from working.