If you don’t miss any historical data in your graphs, you can get rid of this message by stopping your site for a brief moment, running cmk -v --convert-rrds --delete-rrds and then starting the site again.
The command will convert any historical perfdata remaining in the old format and convert it into the new format.
More information is available here: Performance data and graphing - Evaluating measured values in Checkmk quickly and easily