Yes, that would work nicely
Another idea that occurs to me is that you could, before merging the layers, export the relevant layers on their own.
Right Click on the layer and choose Export Layer… from the pop-up menu (it’s down near the bottom of the menu).
And in the export window that opens make sure you use PNG as the file format.
The only down side to this is that such exported layers only contain visual info i.e. how that layer looked at the time of export.
If you then re-import it, it will not have any paint wetness or depth info typically found in Oil Paint for example, which may or may not be important.