I was moving data around like crazy between partitions and external HDDs, just to be able to accomodate that huge database.
If a couple dozen GB are "huge", you might want to get a new HDD/SSD anyways. Ten times the size of the block chain in storage costs about as much as a BigMac menu at McDonald's... Who the hell uses several partitions on one disk these days anyways?
Also reindexing takes a few hours at most on my machine, so probably you're running on something that might not really be fit to run a full node in the first place.