If you are running out of disk space our recommendation would be to use the "Historic Data Purging" settings you find in PRTG under: "Setup -> System Administration -> Core & Probes" If you scroll down, you see the purging configuration. Any value is the number of days for which PRTG keeps the data before deleting it.
Also you can delete old data manually.Bear in mind these entries will no longer be available for graphs, tables, or reports.
To do so:
1) Stop the PRTG service
2) Backup your PRTG data folder!
3) Delete old data files
4) Start PRTG service
Disclaimer: The information in the Paessler Knowledge Base comes without warranty of any kind. Use at your own risk. Before applying any instructions please exercise proper system administrator housekeeping. You must make sure that a proper backup of all your data is available.