Hmm look through tracker logs to see why your messages and call logs disappear every few hours, its very strange for them to keep disappearing. Logs located at /home/user/.local/share/tracker/ Once you have all your data its better for once you reset tracker (tracker-control -r) and let it begin again.
~/.local/share/tracker $ ls -l 2700 tracker-extract.log 95919 tracker-miner-fs.log 166792 tracker-store.log
"Tracker-Warning **: Could not get new ressource ID: database disk image is malformed
Tracker-Critical **: Unknow class http://semanticdesktop.org/ontologies/2007/01/19/nie#lastRefreshed
tracker-control -r