Isaac hi,
You can disable the clean-up notifications totally. Go to Application Menu->Preferences and set 'Cleanup Period (days)' to 0. The notifications will be gone but you can still clean up the history manually, via the Runs History dialog. Note also that there you can lock up selected records to prevent them from any clean-up, intentional or incidental.
The replacement of the data report files would not work, unfortunately. The data reports are stored in a special binary format (non-readable), so plain text files (obtained after converting or exporting) can be accessed by Runs History database. I would recommend to always export all important data reports and store them separately, e.g. on a different PC. In this case, you will have readable data files and their binary backups in the Runs History.