Are you mandated to use a Fault isolation manual when clearing a defect on an aircraft?
FIM contains procedures for both A/C systems (E.G. EICAS, ECAM, CPDS) messages and pilots/maitenance observations (e.g. smell of burning oil, windshield delamination).
All kind of reasonably possible faults should be covered by FIM.

Just simply use yor FIM preambule to determine if it specifies what to do when fault is not covered by FIM and to determine either mechanic judgement or OEM (A/C manufacturer)contact is requied in such case. 
If such information is not included contact OEM.