How are fluorochromes conjugated to proteins such as antibody?
Fluorochromes are covalently bound to the antibodies to form stably labelled molecules. This paper describes it in great detail, from the abstract:


  Fluorochromes can be covalently conjugated to antibodies through
  reactions with thiol or amine groups. Typically, fluorochromes
  containing isothiocyanate, succinimidyl ester, or sulfonyl chloride
  reactive groups are conjugated to amines on the antibody molecules.


These covalent bonds are stable at room temperature and are also at -20°C. It's more likely that repeated freeze-thaw cycles damage the antibody.