The best thing I can think of is to keep a list of the package names that you can copy and paste into your preferences file in the “ignored packages” section. If you have any sort of linter or code intel that might be the culprit if it’s several thousand lines.
"ignored_packages":
[
"SublimeCodeIntel",
"Vintage"
]
Another thing to try would be to just make a copy of your Packages/Users/Package Control.sublime-settings file, then edit the original and delete all the listed packages there and restart ST3. Definitely make that copy first in case it screws up.
Gabriel reports he ultimately solved the issue by copying the list of installed packages out of the Packages/Users/Package Control.sublime-settings file and paste them into the ignored_packages section of his preferences file.