I personally do think (and have seen) that HCl treatment does alter the chromatin signatures. However, the precautions one needs to take are - 1) Keep a positive as well as negative control using other antibodies for hybridization with known/expected patterns/results for that cell line. 2) standardize Cross linking time prior to HCl treatment - so as to preserve the positive control reactions. However, since BrdU staining is a well accepted standard protocol for nuclear staining, you shouldnt have much problem convincing a reviewer if you have used a standard kit or published protocol.

HCl treatment is a common precursor to a lot of nuclear in-situ hybridization assays, many of which use other nuclear markers with little problem. (I'm assuming you're talking about a 'relatively gentle' 0.1N HCl incubation for 10 minutes or so.) As with most things, it will effect some epitopes more than others, so take Subhojit's good advice and include the appropriate controls. Odd are you'll be fine, though, so go ahead and try it out.