This is happening for me too. All my replays are still in the Data/r folder but my local scoreboards that were linked with those replays appear to have been wiped.
Only thing I've done that might be weird that I think could possibly cause something like this is a lot of switching between public and test build in the same directory... maybe saving a replay in a map from the test build? No idea.
scores.db (last modified yesterday) is only 3KB. I also have files called scores.bak and scores.dat.backup but they're from 2009 and 2008, respectively. They're probably useless.
edit: more info. The earliest plays of mine with replays are from 7/24. The last time I played before that was 7/19, going by the files in my Data/r folder.