Nearly all boards have a 'reset CMOS' jumper to wipe the RTC, and still other boards have had the contents lost when the battery goes flat. It doesn't cause any harm, unless you have an old hard drive that needs manual BIOS settings, in which case you only have to put the same settings in or you might have to reformat the drive.
If you're swapping RTCs, it's probably a good idea to either reset the CMOS using the jumper, or at least go into the BIOS setup and load the defaults after putting the new RTC in, just to avoid the potential situation where the old and new BIOSes use the same checksum, and the new BIOS accepts the existing RTC values, which aren't valid for the motherboard.
Unlikely to cause major issues, but if there are things in there like CPU multipliers then you may not be able to boot until they are reset, and the BIOS reset jumper on the motherboard is probably the best way to do that.
Remember that the BIOS reset works by putting a jumper on it, powering up the system, it won't POST, power it down again, then remove the jumper. If you just connect the jumper without powering up the system, it won't erase the RTC.