Or even upgrade to a harder bolt.

I guess the worst thing that could happen is one of the washers digging into the cup and damaging it but as Sheldon said, the cup is much harder than any normal washers you are going to get at a hardware store so the softer washer will deform first. And even if it did damage the fixed cup the only reason to really ever take it out is to replace it with another one or a cartridge BB.