This has happened to me too and it is annoying. However, I believe the delete is a soft-delete unless you specifically configure CrashPlan to remove deleted fil

This has happened to me too and it is annoying. However, I believe the delete is a soft-delete unless you specifically configure CrashPlan to remove deleted files after so many days. I have mine configured to NEVER remove files, even deleted ones. I've found that you can alleviate some of the headache by assigning the disks unique drive names. The reason for the deletion is that you might plug in your external HDD that gets mounted as drive F. You let it finish backing up, then disconnect it. If you later plug in a tiny flash drive that also gets mounted as F:, CrashPlan will see the contents of that drive and assume that you deleted everything from the previous drive and accordingly mark is as deleted in the backup. If you mount the external HDD as drive Z:, however, when you disconnect it, CrashPlan will simply show the device as "Missing", but won't delete it unless something else gets mounted as Z while CrashPlan is running.