When you run the archiveconfig command from the LEM it will backup all of the missing partitions. So even if you delete a third of them at random, the next time you run your backup the LEM should fill in the gaps. If you only need a live retention and backup of a week you can reduce the disk on the LEM so that it stores less data all together:
Resize a LEM Virtual Appliance - SolarWinds Worldwide, LLC. Help and Support
With the reduced space once it runs the archiveconfig there will be less data to back up.