When using the console command “RecreateLandscapeCollision” (after losing landscape collision), all holes in the landscape (opacity masks) are disabled. Visually, the holes are still there, but when playing, you can no longer walk through them.
I was able to reproduce this on my end and have entered a bug report, UE-9875 to be assessed by the development staff. As a workaround for this, after recreating the collision, immediately use the visibility sculpting tool to paint a bit of hole material onto your landscape (it can be the same spot the original hole is located and does not need to be a visible alteration). This will reset the hole to remove collision again.
Thanks!
We are currently using that workaround, and it is working out good enough for now. Looking forward to having it fixed though, as we are making more and more holes, and redoing them every time is going to get tedious.