How to lay out Gerber files for flex-rigid pcbs
Rigid-flex boards are still so outrageously expensive that vendors should be able to work with you to get a mutually acceptable solution.
Last time I did one, I used Altium which has specific features for rigid-flex but I think you could do it simply by laying out a multilayer board with internal (typically) layers designated as FPC. You could demarcate the rigid and flex areas on a mechanical layer just as you would define an outline. Of course the stackup has to be described fully, and any mechanical features such as stiffeners, so either a mechanical layer with a lot of text or a mechanical drawing. I used a proper mechanical drawing with tolerances, showing all the details. The stackup in my case had a core of a polyimide circuit with coverlays in the flex area and FR4 layers on either side in the rigid sections, but there are various possibilities depending on your vendor and budget.