We do have the solution that you can use to fix RRD files when the number of data sources increases.found extra data on update argument
https://support.nagios.com/kb/article.php?id=149
But to answer your question, we don't have anything in place that can automatically delete RRD files if there is a problem. Also, deleting RRD is not always the best solution because It deletes graph history. If a graph was collecting data for 1 year you will lose 1 year of data by deleting the RRD.