I've installed an old version of Indigo (1.0.0 rc2 from 20 March 2023, the oldest version I could find) into a VM, then upgraded it in-app to the current version (rc8a) and it worked perfectly, so I don't think I'm going to be able to replicate this unfortunately.
However, I did have a realisation, which was that the uninstallation instructions on the site were actually intended originally for someone wanting to remove Indigo, but not to reinstall a fresh copy. The latter requires an additional step, so I have modified the instructions as needed. I'd be grateful if you get a chance to try them one more time, noting especially the new part e):
https://indigostack.app/docs/how-to/uninstall/