A physical blockage in a flowcell is very unusual. For something (either particle or chemical compoun) to precipitate in the flow cell, first it has to travel through the injector, then the tubing before the column, through the column, through the tubing after the column, and then suddenly stop in the flow cell. I do not believe this happens very often, but if it does, you may have some serious method problems that should be fixed.
There are two other possible explanations:
1. If your compound is photosensitive, the low wavelength UV light from a diode array detector could cause polymerization, which might precipitate in the flow cell. But this would take many injections, since you are injecting ng each time.
2. The tubing that is connected to the flow cell may be bent. PEEK tubing can develop very high back pressures if it has a "kink." Stainless steel tubing can sometimes show the same problem.