Do you ever run into the issue where you've overridden a dep from the main :deps list in :extra-deps in an alias with a locally checked out version? Usually lsp still looks at the original one, which gets messed up if any changes happen in the local version.

if you don't restart lsp via lsp-workspace-restart , clojure-lsp will use the old classpath, did you restart it?

I don't think that's the reason because my project has been set up like that long-term as I develop a group of libraries in parallel.

if you manage to create a simple repro where I can test maybe we could find the reason, it could be a bug somewhere

Ok, I'll do that, but may be a bit of time before I can get to it.