I didn't understand much of your post. Which battery? If the RAID battery, then it should continue to run, albeit with degraded performance. If it is the CMOS battery, then it should not affect the OS, per se, but certain settings may be lost in the BIOS that may affect what the OS sees, including disabling integrated RAID. The RAID battery is $40-80 and the CMOS battery is less than $5 ... just replace it.
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