I have a couple of Li-Ion batteries I made up for a particular application. They each consist of four 18650 cells in series along with a 4S battery protection board. I have been using these two batteries in series to give me an 8S configuration without any problems. My question regards re-purposing these batteries. I'd like to use these batteries to make up a 2P4S battery but I don't want to strip the cells out of these batteries and reconfigure them. What would be the down-side(s) of putting these two batteries in parallel (effectively paralleling-up the two 4S protections boards)?
If by 'paralleling up' you mean just paralleling the battery + and - leads then it will be fine.
The protection circuit in each pack works independently of the other, so in a fault condition (over/under voltage, over current) one pack may disconnect first but the second one will follow shortly afterwards.
You will definitely want to be sure the cells in parallel have a voltage close to each other before connecting them, otherwise you will get fairly large currents trying to balance the cells as they even out. Other than that there should be no issues. Side note: If you use cells of similar capacity in parallel it helps boost life and efficiency. We started capacity matching cells in one of our batteries that uses cells in parallel and it boosted the specs a fair bit.