Had the same thing with child benefit and my company car at the time pushing me over the threshold for child benefit.
Got demands for £800, that was already 2 years late!
I'm on self assessment so that is actually a separate account with HMRC, one said I had paid off the underpayment, and the other said I hadn't!
Every time I called they were super helpful and confirmed that the outstanding was cleared, and they would send a message to the other department confirming I had done so.
I still got letters and demands, I ended up sending a recorded delivery letter to them, explained the situation and how annoyed I was etc etc, got a letter back confirming I was right and the accounts were settled.
Check if there is a separate "self assessment" account, and if this is showing an underpayment on your online HMRC tax account.
Don't just leave it either, the government is skint, they wont leave it!
Good Luck!