Sounds 2.5N HCL is very concentrated itself for tissue IHC to begin with. You may tell whole protocol in detail than someone can answer you.

I pre-treat the sections with 2.5N HCl for 30 minutes then neutralize the sections with 0.1M Na-Borate (pH=8.5) for 10 minutes. After equilibrating the pH to 7.4 with 1xPBS for 5 minutes I block the sections with carrier medium (1xPBS with 3% BSA and 0.5% Triton X-100) for 30 minutes. After this I add the primary antibodies in the carrier medium.

Yes, Sara, your protocol appears right. I verified.

Denature DNA by incubating sections in 2N HCl for 30 minutes at 37 °C, and neutralize the acid by immersing sections in 0.1M borate buffer for 2x5 min.

So if you use 1M instead of 0.1M that will affect pH adversely. So keep the same as it says.

http://www.ihcworld.com/_protocols/antibody_protocols/brdu_accurate_chem_sci.htm

Good luck