In case anyone else gets this bug again, which I just did, I found a way to fix it.
While playing the bugged stage, without pausing or anything I did a hard reset of my ipad (press and hold down the home and power buttons I until the apple logo appears on the screen), once it had booted up again I force closed the still open app by double-clicking the home button and swiping it away, then started the app again.
I got back to the welcome screen, finally it didn't resume me right into the stage, and when I opened endless in pirate seas it still remembered what stage I was on and my plants, but the broken save that would resume me mid-fight was gone.
No progress lost except the last unfinished stage that got bugged, perfect!
4 years later and this problem persists. I guess no one was ever able to fix it. ☹️
