Problem(s) Encountered:

When closing the dome in the morning. We set tracking rate HA to zero and attempt to point telescope to zenith, but error message pop up  make sure tracking rate is zero first!  Then we were no longer able to slew telescope and dome after DFM program. Manually home and close dome, but telescope is still not at zenith. 

Solution:

Found the TCS showing HA=08:28:51.6 and dec=-5:23:52 when I arrived today.  Obviously there were also flags for APPROACHING LIMITS & LIMIT REACHED.  SLEW ENABLED was also flagged in the TCS,  Telescope position was actually closer to about an hour east and declination of about +60.  Checked the encoders and they look OK, as do the read heads.  I have no idea how the system got into a state where it was so off in both axes.  Muddling through menus, I came across:
Telescope>Initialization and found at the bottom of the window a subsection titled “Set Absolute Encoder Offsets” with two options: a) Zenith Offsets and b) Defaults.  There is also a button to show current offsets, although these did not correspond to anything obvious to me as I had no reference to good values and likely they were nonsensical by this point anyways.  Clicking ‘Defaults’ gave me positional values that aligned (at least roughly?) with telescope positioning.  This also as expected cleared the limit flags.  I could then stow the telescope to zenith.  
Running tests, all seems ok with the TCS, telescope & dome and its connection with JSkyCalc.  Unfortunately, I do not know how long ago the encoders were reset to default values, nor do I know how much they may have been offset over the last many years.  Making note of the current offsets, values now are:
HA=10.458 DEC=213.395 at zenith.
It is likely that the user will have to move to a bright star and zero out errors at the start of tonight.This is also a good reminder that we likely would really benefit with updating the telescope pointing model soon.