Custom Lint Looking For Deleted Subpackages

[getBoolean]

Describe the bug
I recently refactored my project to reduce the number of sub-packages in the project, and now custom_lint is failing since it can't find those packages.

Logs:
custom_lint.log

To Reproduce

Can't reproduce in a separate project, seems to be cache related since cloning the git project doesn't reproduce the issue either. I've also tried flutter clean and dart pub cache clean but it did not help.

Expected behavior
Cached sub packages should be able to be cleared