The largest one that I was ...

The largest one that I was involved with is Jeddha Phase 3 (240,000 m3/d) in Saudi Arabia for SWCC.  Their requirements for 2nd pas RO is to limit the chloride level to 60 ppm.  So there were partial bypass of the main stream (1sp pass RO permeate) that was treated in the 2nd bypass and re-collected in a secondary tank. 

2nd pass RO will also give you the flexibility to schedule maintenance on a large 1st pass RO on your time because the water treated in 2nd pass is going to always lower than 1st bypass RO.  If something to a 1st pass and there is no 2nd pass, you must investigate the source of the problem immediately and fix the unit right away.