How can severe wear conditions be detected if the larger particles that are produced in these situations are retained by the filters?

We have to go where the evidence is...if aggressive fine fltration is in use the next step is to remove the debris from the filters / chip detectors / magnetic plugs and examine it.

Spectroscopy and ferrography are always limited by any filtration technology that removes material from the oil.

Systems will have different size filtration, gearboxes in particular will not in general have fine filtration so will benefit most from particle analysis.DR Ferrography will be useful as it will detect larger ferrous particles than ICP spectrometry which only detects particles ~7 micron or below.
The basis of OCM is trend analysis so failure mechanisms will generally be identified even with filtration.