[David Cutler]

If you have the layer names in a custom column @Vince you could filter by that layer name, “water” for example and then select all and reestablish the layer that way.

Unfortunately that doesn’t solve the problem of the layer assignment getting wiped from the tool, but it might help re-establishing the layers on markups that you have already placed.

I’m guessing that you are probably doing something along these lines already, but thought I’d throw it out there just in case. 😎