Hi Pete and John,
the minimum exposure time depends on the frequency f of the power converter's AC output which supplies the EL foil / the LED's.
If the exposure time is less than approximately 1/f, this may result in a highly uneven illumination. So the lower limit for the exposure time of the flats should be approximately 1/f (or somewhat higher). The frequencies of different types of power converters may vary greatly. However, I guess there will be no power converter with a frequency less than 50 Hz, so exposure time greater than 0.02 s will be OK in either case (1 - 2 s definitely will be fine). If the frequency is not known you can try different exposure times and judge from the evenness of illumination, which minimum exposure time is necessary.
An alternative to inserting another layer of polycarbonate would be, as Rob suggested, to lower the gain (for the flat frames and the flat-darks frames likewise). However, dimming of the EL panel is either a provided feature of the power converter that was delivered with the EL foil / the LED's or it may not work at all. Simply decreasing the voltage is no option because that normally does not work reliably.
Bernd