Any difference in voltage between the batteries will cause current to flow
from the higher-voltage battery to the lower-voltage one.

If this makes you feel uncomfortable, it should. It's not a good idea to run
batteries in parallel, unless there is some mechanism (such as a series
diode) to block this flow.

Lithium coin cells aren't horribly expensive, especially if you buy from a
mail-order supplier. You can use the opportunity to stock up on batteries
you need for other stuff you own.