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Not a guru, but similar situation by ndaero93

My wife's plan year runs 1/1 - 12/31 and mine from 7/1 - 6/30. We used to both take some out, but the accounting was mess as our expenses didn't line up.

If I remember correctly, when I had a bit more than was allowed, I just paid the taxes on it. So, if you know you are going to have 10K in expenses for the year that you can get reimbursed, you should probably be OK - if they are valid expenses and you ARE NOT getting paid for them 2x (i.e., claiming the same expense against both accounts), you are not breaking any rules. You are, however, under-withholding taxes and when you do your forms in 14 for Tax Year 2013, you'll owe a chunk on that $5000 that should have been taxed.

You can, always go back and up your withholding if you don't wan to owe at the end.

NOTE: I am a taxpayer and not a preparer or an Accountant. I do, however, know that Turbo Tax led me through this a few years ago.