My Wife's a Taxman, and they still got mine messed up - once.
Best advice is to compile all your evidence into a letter. then Phone them up and talk to them telling them (politely) what your case is and what you would like them to do. In most cases they will want a letter (like MOD they don't trust those electric mail things) from which to start their review of your casenotes.
Keep copies of everything you send and only send originals by registered mail.
I am reliably informed 'they' can officially go back 9 years, but in some cases...
Best of Luck