I had new heat shield brackets welded on last year so I could reattach the heat shield and now need to remove one of them temporarily  so the hole underneath the bracket can be welded shut to stop an exhaust leak. There is the hole that goes thru the muffler that I was going to have closed, but there is also a second smaller hole beneath the  first one, should I try to leave the smaller hole open or does it not really matter?  What were these holes for?

Flip - far as I know, there shouldn't be any holes through the muffler walls as these will give exhaust leaks and increased noise as the exhaust gas will take the easiest path to atmosphere (avoiding the baffles). It is surprising how much pressure does build up in the muffler. I had a hole appear in my original stainless exhaust on my previous K - tried to patch it with off the shelf exhaust repair paste, tape and every other exhaust repair product from my local auto store - waste of money, it just kept blowing after a few runs and, in the end, I got myself a complete second hand exhaust and fitted that (complete with the saga of having to drill out 6 of the 8 exhaust header studs that sheared off during removal!).

It may be that by welding on new brackets last year that you have either burned through the muffler or created a heat affected zone that has caused accelerated corrosion which has resulted in pin hole leaks (which get bigger over time). Yes stainless steel does corrode (just not as quickly as mild steel) and can be badly affected by salt (causes crevice corrosion and/or cracking)

Ok, I will have the hole welded shut,thanks.     I don't know if the muffler was switched from another bike possibly but these holes look like they came from the factory as they are nice and clean and uniform . I don't have a photo right now but I was wondering if the small hole was threaded.

https://www.k100-forum.com/t1411-installing-a-bmw-muffler-repair-kit-p-n-95009000390

Has it had one of these kits fitted?