Maybe you could rename the channels for the patients you want to flip?
Right-click on the channel file > Edit channel > Edit the labels manually to exchange all the pairs of symmetric electrodes (eg. rename Fp1=>Fp2 and Fp2=>Fp1), then save the modifications. Do not keep two channels with the same label, this would cause lots of problems.
If you do this, you wouldn't be able to average directly the EEG measurements for all the participants together because the list of channels would be different. You'd need to rewrite all the modified patients files to actually exchange the EEG signals in the data files. You can do this by selecting in Process1: first one unmodified patient, and then all the modified patients, then run the process "Standardize > Uniform list of channels > Use first channel file in the list".
Does this help?