Welcome. Do you mean that the insert has an actual hole in it? Replacing that insert is probably your best bet. See if you can locate some inserts and glue a new one in.

Sounds like to need a new lens from a scrap playfield somewhere.

To replace it:
On the top side carefully cut around the lens you need to remove (modelling knife & ruler or anything you can think of the make it neat). That makes sure you don't damage the surrounding area when you remove it.
Then clear anything out of the way below the area for access and heat the underside up until it is pretty hot and knock the insert out from below. You can use a decent hair drier for that as you want it hot but not burning hot.
Then clean up the hole and the replacement lens if 2nd hand and glue the insert in place it so that it is level. Job done.
Personally I would just like with it until you find a replacement before starting.
I don't know if that is the proper way but it worked for me on my Funhouse and others.