Saving the time from the standard WB time program (in prefs) should write the time and date to the RTC.
If you have a multimeter handy, turn the machine off and check for at least 3V between pins 18 and 9 of the RTC device, U178.
If you have a scope or counter, check for approx 32kHz on pins 16 or 17 with the machine off. That gives a good indication if there is battery power there and the clock is running.
You might also try replacing the clock's data latch, U177, as this sometimes causes clock read/write problems.
Obviously you'll need access to SMD rework equipment for this.
Hopefully you haven't damaged the RP5C01 clock, as these are obsolete and can be hard to get.
Anthony.