The sort of settings that will be lost include
Startup Boot disk selection
AppleTalk on/off status - doesn't matter on systems with "Open Transport" installed.
Disk Cache size setting. (Defaults to 32K).
Cursor Blink rate.
International Map setting.
Current Date & Time
Highlight colour setting.
If none of these worry you, then it doesn't matter. Note that if you booted from a second boot drive, when the battery goes flat, it will boot from the FIRST logical boot drive.
Also, with respect to the AppleTalk setting, if you had a serial printer connected, when the battery goes flat, your printer won't work until you turn AppleTalk off (unless your printer is using the AppleTalk protocol). For serial printers, often the "cheap" solution was to configure the printer to use the "Modem" serial port, since Appletalk never defaults to the modem port.
Date & Time and international Map setting can (and does) cause problems with date-stamps applied to outgoing emails, such that the receiver of the email might see the year the email was sent as "1970".
Additionally, it can make some internet security certificates appear to be expired when in fact they are not.
Note also that file "Date Created" & "Last Modified" date & times will be erroneous.
So... it depends on what your needs are.
On a side note, a battery that goes flat in some models (LC475 / Quadra605 , PPC 6100 & PowerMac 7220 / PowerMac 4400, iMac Tray Loaders) can make the machine look like the logic board has failed even if your replace the dead battery. The trick is to remove the battery, AND ALL POWER SOURCES, and short the battery connector's terminals out overnight. Many "authorized" dealers got caught out with those.
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