How can I use tmutil to figure out which files just got deleted?
Run

tmutil listbackups


to get the list of snapshots available. Pick the one before the problem occured and run

tmutil compare YOUR-SNAPSHOT-HERE | cut -c33- | grep /Users/YOUR-USERNAME


to get a list of differences between then and now. If you leave out the cut part you may also get some indication concerning the actual difference (but it's more difficult to use the result afterwards).