First a disclaimer: I do not know the 734 or the CFM56!
(BUT) If the 734 fuel system is similar to the rest of the Boeings the boost pump pick up 'filter' would be nothing more than a VERY coarse strainer so it would be unlikely to clog*, and possibly (if it did) the first hint would be a low pressure light/warning from the affected pump itself.
There are a number of reasons for FILTER BYPASS and if no fault is found with the filter itself (it may need tearing apart to see if it is contaminated)another possibility could be ice forming in the filter from cold fuel. A good case for thorough water drains checks!
Next stage would be changing the diff. pressure s/w. and more remotely a wiring fault/chafe somewhere!
I would hope that the filters are replaced on a regular basis.
As for the high speed abort, probably the wrong call but it would depend on your procedures.
*It is designed to stop the odd fitter/poly bag/carpet/rag/nut/bolt/washer from getting as far as the pump impellor!
