What does resetting to factory defaults reset? What does reflashing the hand control (HC) and motor control board reset?

Using Menu > Utilities > Factory Settings will reset your time-site information including city, time zone, etc. and much more.  Here are the items that default:

GPS on/off
Direction button (positive and negative on both axes)
Scrolling speed
Calibrated altitude software stop (Alt-Az mounts only)
Home switch Calibration (both axes) for the CGE and CGE Pro mounts
Tandem mode setting
Meridian mode setting
Calibrated GOTO timings
Keypad backlight level
LCD backlight level
RTC on/off
Last location (city, longitude-latitude, time zone, etc)
All the settings saved when you last hibernated
Filter settings (east and west)
Sun menu on/off
User land objects
User sky objects
Camera settings (4/5SE only)

When you do an alignment, small errors in the mount's physical geometry are measured and corrected.  They are stored to facilitate finding the alignment stars the next time you align. These values are reset to zero.

When you do the factory reset in the HC the results depend on the version of the HC firmware you are using. Starting in version 4.15, you will lose all settings saved in the motor control as well as all settings saved in the HC.  Prior to version 4.15 you lost only those settings in the HC.

When you reflash the hand control to a new version number you will restore to factory default all settings saved in the hand control except the language setting.

If you reflash the motor control board to the same or a new version, these settings will be reset:

Anti-backlash settings
GOTO approach
Autoguide rates
Limit switches on/off (CGE and CGE Pro mounts)
RA (slew) limits
PEC recording (GPS, CPC, CGEM, CGE and CGE Pro mounts). Use PECTool to save your current recording before the upgrade and restore the recording after the upgrade.

Updated 12/27/13