Vortex requires permission... error when trying to deploy Skyrim mods.

[Semak0]

I had a working mod list for Skyrim, with a couple hundred mods. Everything worked fine, until my system SSD broke down. I got a new SSD, reinstalled Windows, Steam and Vortex and restored both the steam folder and the AppData folder from a backup.

When I then started up Skyrim, it worked fine and it seemed that all my mods had loaded correctly.

However, when it came to installing some new mods, the problems started. Now whenever I try to deploy, I get first a popup that several files outside of Vortex changed and whenever I either choose to keep the changed files, I get the error message that Vortex needs permission to a certain folder from a certain mod.  When I manually navigate to that folder and check its properties, I can see that it is write-protected (but otherwise there are no restrictions in its permissions, equal to chmod 777). When I remove the write-protection, it gets reset immediately.

Also, Vortex ends up in an endless loop, as whenever I try to click the error popup away, it reappears and the only way to stop Vortex is to kill it in the task manager.

How to resolve that issue? I would prefer to keep my modlist instead of having to start from the ground up.