For anybody who comes across this thread in the future with a similar issue:
I wasn't able to ultimately figure out how this occurred but I decided to remove the E:\ pool from the D:\ pool using the default removal settings and that removed the extra drive letter. A SnapRAID scan of all the constituent drives that comprise my E: pool didn't find any unexpected changes, so it appears to have been a safe operation given limited testing.
Tiru got a reaction from Shane in Removing a nested pool