Technically, vexillology should be for questions on the study of flags (e.g. "When did vexillology become a recognised field of study?", while flags would be for the actual flags (e.g. "Why was red chosen in flag x?") Obviously, in practice everyone use both to ask about specific flags only.
I have therefore merged the two flags without making them synonyms. If we do get a question on vexillology the study, we can properly tag it vexillolgy, but that tag is destroyed in the meantime.