I had the same issue and what fixed it for me was booting up the game, clicking Mod Manager, then clicking Open Mods Folder. This brings up the location where your mods are installed, then I went to VintagestoryData, then I opened the clientsettings.json in notepad++ and scrolled aaaaallll the way down to the bottom where it says "modPaths". The path you're editing should roughly be at the very bottom, for me it was line 295 but that will change depending on how many mods you have installed.
*Note: You'll want to exit the game before editing the json file otherwise it'll just undo what you are about to do.*
I decided to go with a different user name on my new pc so all I had to do was change the "C:\\Users\\Old user name\\AppData\\VintagestoryData\\Mods" to my New user name on the new pc and then saved, booted back up the game and bam there they are. This might not help others but cant hurt to double check that the user name is correct in that file path.
I think this is what 321BoltsOfLighting was getting at back in October. I would also recommend only editing the file path unless you know what you're doing.
I hope this helps, good luck out there peeps, there be bears in them woods!