Refreshing a Citrix profile removes any system settings that individual user has created in the program. This does not remove any data or information created, however does edit the preferences which does include but isn't limited to color preferences, file locations. 

In the Raiser's Edge, the system settings set in Tools > User Options will be reset to system defaults. 
The Citrix profile's regional settings will need to be reset if any changes have been made.
Recently accessed records will be lost however will start reloading when opening further records.