If they cancel any, it'll be EWR to bring things back to how they are right now. Right now they're operating a non-stop and the direct with stop in FRA, both out of JFK.

Hard to say whether EWR will be canceled or not for June. Right now they have three flights on the schedule for June 8. Seems somewhat aggressive but travel situation in SIN is improving quickly.

If you book the non-stop out of JFK you will definitely fly out of JFK on some flight. The worst possible scenario might be that they go back to non-stop out of EWR and FRA stop out of JFK and you end up being moved from JFK-SIN to JFK-FRA-SIN. Seems unlikely to me.

Personally, I would be opting for the JFK-FRA-SIN flight on-purpose because it'll be the A380 and it's going to be the V3 seat layout which I would consider preferable to the A350 out of EWR. But if you're staying overnight, morning departure of EWR might be better for you.