This is very much an edge case, and perhaps not worth fixing. Could also be caused by my custom compile of Fossil 2.10 for Windows, but I figure I should report this and see if others see the same behavior.

Create a new empty repo using Fossil 2.9. Open a checkout for it. Add a file to the checkout (content and size doesn't seem to matter). Switch to using a Fossil 2.10 build, and for any Fossil command issued you should receive 'Unresolved RID values: 0'. Once you either fossil delete or checkin the added file the error will go away.

This error does not show up on repositories that are not empty. That is, if I have at least one non-empty checkin already present, switching the version of Fossil only causes the 'WARNING: The repository database has been replaced by a clone. Bisect history and undo have been lost.' message to appear, which I am ignoring at this time. This holds true even for repositories with pending changes not yet checked in.

Thanks.