You can't pick & choose which stores you want to delete from.
However, if you want to remove stores, you can do this:
- Delete from all stores.
- Immediately after Step 1, re-upload your album--but choose only the stores you want
Because stores take the same amount of time to delete albums as they do insert new albums, you'll have minimal overlap; your old release will be deleted around the same time your new one is inserted.
If you have a bit of overlap (where multiple versions of the same song are in stores at the same time), it doesn't cause any accounting problems or otherwise.