No expert on this but I am rebuilding two sets of French doors (see earlier
post) for my niece's house. What I found is that if the threshold (sill) is
rotted out, the bottom of the window panels and the door jams may also need
repair. I think it would be far easier to take the assemblies out, do any
repairs, then reinstall them. A couple of pieces of ply screwed down over
the opening would cover the hole while you did a proper repair.