We just upgraded our basecamp and klok accounts so we could use the synching features. The first full synch went well. However, when we tried doing another full synch, it put many of to do items in the archive that were not checked off yet (in basecamp) and added in a bunch of client names (that were from old archived basecamp projects) to the project list. It gave an error message (something about moving some archived items) when the full synch was done.
My assistant said he found a workaround, but it makes the process of adding a new item to basecamp (and then getting that item into klock) painful:
"It seems like if I restart klok and the first thing I do is a full sync before anything else it doesn't move stuff around, except of the to do items I just checked off."