Yes it will start to damage the seal. You can flip it if you want, but i think it happens even without doing so due to solvent vapors. Although it takes a little while for it to have any noticeable affect.
This is the reason i won't use mason jars with limo anymore. It happens with naptha too, but limo especially will damage the seal and begin to leak out. I have a feeling that its not to healthy to have this happening, especially when you wash and reuse solvent over and over. Contaminants from the seal dissolving will build up over time. Not to even mention the paint on the bottom of some mason lids.
Sep funnels and GG stoppered glassware is a good investment. Mason jars work if you only plan on doing a few extractions, but all glass is really the only way to go in the long run imho.