Hi, this seems to be a little different problem than the one Logos reported to me a few days ago.
In fact, this has a pretty easy explanation. The paths are stored in a way that kernel drivers understand them. So, and as you can verify, there are no drive names in the rules.xml file, where the rules are stored, instead links to the partition numbers on the disk are used instead of the drive names.
This is easier for the kernel component to find the files, and also gives some extra flexibility - when drive letters are changed, as long as the partitioning remains the same, the rules are still valid. In your case, however, adding and removing that external drive changed the partition numbers so much, that the entries were no longer found on the disk (i suppose you must have started the system once from the backup drive and let the rules be populated from that partition, or the disks must have somehow changed their places, boot order, etc.
So, once booted, your C: drive referred to e.g. the partitionnumber3, after reboot and disk configuration change, your C: drive ended on partitionnumber2 and 3 was now your drive with the letter S:, latter again with the disk removed, you ended up with D: letter occupying the partition with that number.
There are several disk identifiers available for the developer to choose from, either disk letters, partition numbers or even partition guids. For this specific example, I guess disk letters would work better, but there are other situations, where you might find nice that you can change the drive letter without invalidating all the rules.
Lukas