I have a couple of thoughts, depending on the solubility of your compound in different solvents. Please forgive me if your tried these already.
One is extraction (water/ Dichloromethane or ethyl acetate); your compound(s) are in the organic layer and the acid goes into the water.
The other idea is solid phase extraction, and this works with compounds that are water soluble- the link goes to an app note where I had to remove salt from a compound I purified with an ion exchange column; the compound, a dye, is quite water soluble. Although I used an automated flash system, the method could be adapted to other equipment as well such as prep HPLC or open columns: http://www.isco.com/WebProductFiles/Applications/101/Application_Notes/AN95_C18Aq%20Desalting.pdf
Depending on what sort of chromatograpy, maybe just load the sample and run it . If doing reverse phase chromatography, run a gradient starting with a low concentration of organic solvent; the compound stays on the column and the acid gets washed out. This is sort of combining my app note with the follow-on purification.
Thank you for your answers. I hope neutralizing with a base and run through Ion exchange columns might work well. But again, I forgot to mention this before, my sample contains sugars which, as we all know, are highly soluble in water so RP columns not going to help me here. So my only alternative would be ion exchange chromatography which I can try. Thank you once again for your helpful suggestions here.