Dear Anjali Krishna G that's certainly an interesting question. However, it's very difficult to give you a qualified answer without knowing which particular Schiff base you are talking about. I suspect that upon complete evaporation of the solvent you had some enrichment of colored impurities. I assume that you will get the original yellow color back when you recrystallize your product from e.g. hot ethanol. The colored impurities will then stay in solution.

Would pH shift be (part of) the answer?

We see in drying buffers that pH shift occurs, as the water is removed, the acid or base changes it's pH as the H+ have different mobility. This is a big problem for those drying peptides and proteins from buffer, where pH shift is seen when freezing, also. For an visual, take some phosphate buffer, add some universal indicator, and freeze it, watch for the colour change.

Kind regards,

Rob