Yes, the alternate system should work if it was an indicator asymmetry fault.
As for the alternate system failing, it could well be the air loading on the flaps combined with the alternate drive motor being old, as I can only assume that after the indicator replacement both systems tested fine and a detailed inspection was carried out of the flaps for damage or FOD etc.
If it turns out that it was definetly an indicator problem giving false asymmetry signals after its overhaul/repair I would urge your engineering department to replace the alternate drive motor as a precaution.