I upgraded a old 2600 router from 11.3 to 12.3

it shows the system software as 12.3
but the bootstrap is still 11.3

how do I change that? Does it matter?

The bootstrap on the older routers needed a chip swapped out to upgrade. You can search on ebay for "cisco 2600 boot rom" to find the upgrade. They are about 5-10 bucks.

However if the router is booting, I don't think it matters. The only reason I know of upgrading the bootrom on that series router is that it allows you to run more memory.