What I is do is

A. not pay any real attention to the flex contribution when it comes out (well, it does show in Quicken for me)
B. when I pay a bill, I take it out of medical sinking funds
C. when I get reimbursed, it goes back into medical sinking funds.

I like having a bit of a buffer in my medical sinking funds (but we’re on Baby Step 7 so I’m not trying to pay off bills).