All of my mods are not managed by Vortex

[Odylarian]

All of my installed mods for Witcher 3 are listed twice in the "load Order" screen. They have a message telling me they are not managed by Vortex and they are loaded again without the message. Oddly, if I disable the mods that are NOT managed by Vortex (by unclicking the checkmark in Load Order), Vortex tells me to run script manager again. So I do, but script manager comes up blank like all my mods have been disabled. Shouldn't Script Manager recognize the mods that ARE managed by Vortex. It is like the mods that are managed by Vortex are not visible to Script Manager.

Also, oddly, when I install a new mod using Vortex, it installs it twice (as managed AND as not managed).

Some background:

1. I have the GOG version of W3. Not that that should matter, but just for total transparency.

2. I have the original W3 AND the GOTY W3 (it was a free download from GOG a few months ago). They are both installed in separate directories under a "C:\Witcher 3" Directory. Oddly, GOG put the GOTY version as a subdirectory of the original game. Therefore, the original GOG W3 has its own Mods directory and the GOTY mods directory is in a different directory than the original mods directory.

3. I can see from the creation dates of the mods in the GOTY mods directory that they are installing in the correct directory so my Vortex directories are set up correctly.

4. Rather than set up a new profile for the GOTY version (maybe I should have), I am using the same profile as the original version. Shouldn't matter, the profile doesn't have mod location information - the "Managed Games" listing has the mod directory information. I changed the mod directory in the "Managed Game" listing.

5. The Staging directory and downloads directory for the mods are the same for both game versions. Shouldn't matter because the GOTY mods are being installed in the correct mod's directory. Since I changed the mod directory location, NO new mods are being installed in the original game mod directory (I checked).

 

Any help is appreciated.

 

[Odylarian]

I think I may have figured out what is causing the "Not managed by Vortex" message but I don't know how to stop it from happening. Here is what happened. Because of this issue (commented above) I reinstalled all my mods and merged them which did away with the "Not managed by Vortex" issue. HOWEVER, when i started the game I got a couple errors. Both errors said a script in the "000merged" mod had some coding issues (ending bracket not matching starting bracket). So, I directly edited the scripts with the errors in the "000merged" mod directory. I fixed the issues but now I get the "Not managed by Vortex" message on all my mods.

If I can't fix the compiling error in the "000merged" mod without causing this issue, how do I fix the errors? Is this a 'bug' with Vortex thinking the mods are not managed by vortex when they really are?