I found the way Cursive achieves this to be a little flakey at an IntelliJ level. If you close your project and re-open it, does that fix it?

(it’s not required to completely shut down the IDE to test this, just close the project, although completely restarting is one way to achieve it).

I've experienced this too, closing and reopening the project (mostly) seems to fix it, and then project seems to stay OK.

Yes, that’s been my experience too. I suspect that it might still be flakey when adding new deps, for example, but I don’t do that often enough to be sure.

Hopefully if it is, reopening the project would help with that too - I expect so.

Closing/reopening didn’t help. I could try deleting the IDEA files/dirs and reimporting. I’m not sure if it’s related, but it wasn’t even identified as a deps.edn project at first. I was tearing my hair out for a while trying to locate the tools.deps window, but cycling the power fixed that, at least.

OK, I wiped the IntelliJ files, reimported, toggled checkmarks a bunch, opened and closed several times, and eventually it figured it out.