EDIT: Since I posted the reply below I've added a function to my thread utility (linked in my signature) which should make it easier to find and copy your orphaned thread files to your current Fusion thread folder.
Ok, I'm back now. So, first of all lets try to find your thread files. I don't know if you're on Mac or Windows but I only do Windows. Open up a File Explorer window and type (or copy & paste) the following into the path field:
%localappdata%\Autodesk\webdeploy\production
You should see a bunch of folders like this:

The most recent is usually the current active Fusion folder and the others are (mostly) previous Fusion locations. Your 'lost' custom thread files should be located under one of these previous folders. The thread files reside in the following location under one of these previous folders: \Fusion\Server\Fusion\Configuration\ThreadData .
Once you've found the files, you need to copy them to somewhere that ThreadKeeper can find them. There is a default folder where ThreadKeeper looks for custom threads but this can be changed to another folder if desired. For instance you might want the folder to be on a network share or cloud drive if you want the thread files to be shared between computers. Copy or move the thread files you found into the ThreadKeeper thread folder and next time you fire up Fusion TK should copy your custom threads to the new Fusion folder for you. Now it's all set up TK should automatically perform the copy for you whenever Fusion receives an update.
If you have any questions just let us know.
If this answers your question please mark the thread as solved as it can help others find solutions in the future.
Marcus Wakefield
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I've created a Windows application (and now Mac as well) for creating custom thread files for Fusion. You can find out about it here. Hope you find it useful.
If you need to know how to offset threads for 3D printing then I've created a guide here which you might find useful.
If you would like to send me a tip for any help I've provided or for any of my software applications you've found useful, you can do this via my Ko-Fi page here.
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