The configuration is stored in NVRAM and the NVRAM battery is actually a Dallas Real Time Clock Chip, located at U4 on the motherboard.
This problem is discussed here: Re: Atlas 550 Loses Config
This discussion has a suggestion on where to buy replacement chips, as well as a link to a video on how to replace them: Replacement nvram clock chip for Atlas 550
I strongly suggest replacing the old chip with a socket and plugging the replacement into that socket. Otherwise you'll be doing it again in a few years. The same issue exists with early Sun workstations and some early Cisco routers, but their Dallas/Mostek chips are socketed from the factory.