duplicate files

[LeapinL]

I am getting a warning from Vortex that many of my files are in two folders. This is for Fallout 4.

This is what it says:

The folder file with hashes f5746510fb7499db and 30565af0bbb68c667 in G:\Steam Library\Steamapps\common\Fallout4\Data\workshopframework_scriptoverride-Man.ba2 are present in another BSA.

It goes on to list this warning for all of my plugins.

I searched my files and I have Workshopframework_ScriptOverride-Main.ba2 in my steam library and in my vortex mods folder.

I just need to know if this is a problem and should I delete the duplicate files or just leave it be.

Thank you,