Yes, you can take dark flats separately from the flats, as long as certain conditions are met:

Match the Exposure Duration:

The dark flats must be taken using the same exposure time as the flats. For example, if your flats were taken at 0.002 seconds, your dark flats should also be taken at 0.002 seconds.

Match the Sensor Temperature:

For best calibration results, ensure that the dark flats are taken at the same sensor temperature as the flats.

While the Ekos Capture Module can auto-generate dark flats during the same session for convenience, it is not a technical requirement. You can manually capture dark flats at a later time — just make sure the duration and temperature conditions are replicated accurately.