The representation of time-series data in FieldTrip requires that all channels have the same number of samples, since the data is stored in a Nchan by Nsamples matrix.
EDF files can have channels with different sampling rates. By default the channels with the most common frequency will be read and represented by the low-level functions ft_read_header, ft_read_data, and by the high-level ft_preprocessing function. Using the chanindx option to ft_read_header, you can specify another subset of channels from the original EDF file. To represent all channels in a single FieldTrip raw data structure, it is necessary to up-sample (i.e. interpolate) the channels to the highest sampling rate.
The edf2fieldtrip detects all sampling frequencies, reads the channels, up-samples and concatenates the channels in a single data structure.