Yes you could do it. Only Regulation E finds "magic" in monthly statement cycles.
While disclosure of the statement period is not required by Regulation DD, I think the change in the circumstances under which the fee would be imposed would be subject to advance disclosure. (That could be debated, but let's just say I would do it no matter who disagrees.)
There is an array of possibilities and you may find it difficult to square the language you use in your disclosure with your EDP capabilities.
For example, if your fee is not assessed based on a balance failure in the statement cycle, it appears to me that you would have to focus on the calendar month as the relevant period. If your statements are on calendar quarters, that should work. I can think of a couple of variables that would make it a lot harder.
Alternatively, you could simply impose a fee every time the balance fell below the minimum; e.g. if it fell below the minimum two times during the statement period you will assess two fees. Six times? Six fees. (This option would definitely require advance notice as it could amount to increased fees.)
Think it through and do a good job with the new language describing the circumstances under which the fee is imposed.