I had exactly this a few months ago. I called and the (very knowledgeable) agent knew immediately what was happening.

Balance is due at 4 weeks out for short haul and 7 weeks for long haul but the wrinkle in the system happens when there is a short haul connection (say UK to LHR) at the start of the trip. The original booking views the trip as short haul based on the first flight; the reminder ‘system’ sees a long haul flight and thinks 7 weeks.

The agent told me I could ignore the 7 week reminder and pay by the 4 week date and it would be fine, which it was.

Of course, I’m offering no guarantee or warranty if your situation unfolds differently!!