I seem to have found the answer. After I wrote the post, I realized there is a Tizen-data folder next to the Tizen folder (for me, both in C:).
I deleted the entire Tizen-data folder, and then debugging worked again. There must have been something corrupted in the emulator itself.
You’ll need to create new emulators in Emulator Manager, and go back to Tools->Options->Tizen and re-enable “Sign the .tpk file…”
I hope this helps someone.