Unless the batteries have been abused I would keep them in and not replace them. The track record on aftermarket batteries is horrible. If you replace all 40 there's a good chance that 10-15 of them will have a sub par/ faulty replacement battery.
If you are replacing all of the digitizers just take some time and test the battery before sealing the ipad back together. Yes it is more time and labor intensive but you will likely find that the original batteries are still fine.