It would be very unusual to have a clog in the return line since is after the filter. The only thing that could clog a line is part of the plumbing that may have broken off but that is pretty rare. Did you have any plumbing work done recently? Also, if you did have a clogged return line, pressure would be higher than normal not lower than normal.
But again, if the filter pressure is lower than normal, that indicates a suction side clog and if the pressure only drops when the skimmer is engaged, it has to be in that line. However, pressure will normally drop by a few PSI when shutting off one of the suction lines so is this something you remember seeing before?