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bbfa235
(Get the code!)
So it sounds like it is a bug that occurs when you do a merge while you have a pending merge.
A few interesting things...
'bzr merge' is designed to not let you merge in another branch while there are pending changes (unless you supply --force). However, in this case you ended up with only a pending merge, which showed the working tree as clean. I'm not sure if that should still be allowed without --force.
However, that is a separate issue.
What *specifically* did you delete under '.bzr/'. You almost *never* want to delete something in there, and I'm not sure what was writing a '.project' file.
It is possible that the file contained information about what revisions were merged, etc. And so when you did your work later, it could no longer access it (and thus failed not finding empty-string revision.)