How do I deal with Seebeck Effect while measuring resistance with 4-lead ohmmeter?
If your generating a negative voltage on the ohmmeter, then yes it's most likely thermoelelectric. My reasoning is I see this all the time when I'm measuring peltiers that have a thermal gradient across them and are generating a voltage with my meter.
The effect is usually measured in mV but usually uV (here for solders on copper) and results from a thermal gradient across a metal. The easiest thing to do would be to put the meter on mV and see how much it changes.
If you really do think it is the thermoelectric effect or have a problem with seebeck voltages, then raising the voltage while measuring resistance would get you well out of the mV's that could be generated. So do a 4 wire measurement and use 5V or 10V (if the device under test can handle the current). make sure the leads are placed as close as they can to the DUT.
Another thing that would help is use the same metal for the contacts because dissimilar metals usually make the best thermoelectric generators. (like use copper on copper.