Does denaturing proteins lead to loss of epitopes?
Many but not all B cell epitopes will be destroyed by denaturing.  Those that are conformational will be destroyed, but there are also many B cell epitopes that are linear, based on amino acid sequence only without strong conformation dependence.  

Also, depending on your IHC protocol, there's often a fixation step that involves a certain amount of denaturation, though rarely as drastic as in immunoblotting.  Conversely, some proteins are capable of at least some restoration of native conformation after they bind to your blotting substrate.

Bottom line, it's unpredictable, but it works often enough to make it worth trying.