I got investigated by the Inland revenue concerning tax relief on NVQ's whilst going through flying training. I had been totally honest and had nothing to hide but the sums involved were several thousands of pounds.
The guy who investigated me was a prat! Fortunately I had photo copies of everything and even had to get statements from the CAA confirming all my exam fees for flying and ground exams.
In the end I threatened him with a formal complaint of my own and sent him a list of telephone numbers of all the schools I had flown with and told him to call them direct.
In the end they owed me a few hundred pounds. Get professional help if you think there could be an "issue" concerning your tax!