Property being sold 'as is' and lender is requiring borrower to pay for repairs (broken windows) prior to closing as a condition of the loan. Should the repair cost show on the GFE? and what line should it go on the HUD1?

You're already past the original GFE, right?
So what you're asking is if this is a changed circumstance that would allow a redisclosure, right?
I think it would fit in the definition of 'information not known at the time of delivery of the original GFE'.
It's similar to finding out you need a survey or pest control inspection.
That said, the chances that your bank has a contracter provider list is non-existent so this is not going to be subject to any tolerances so there is no need to redisclose.

I don't believe repair costs are a settlement fee that need to be listed on the GFE. They would be listed in the 100s of the HUD-1.

I have also believed that repairs were not settlement charges but I am trying to remember what my basis for that belief is. What is your justification for not calling them settlement charges?