If I understand your question correctly , it is the bypass mode and compression mode you are talking about.
Bypass mode is used usually during debugging any simulation failures. especially when chain test is failing in compression mode. In compression mode serial simulation failure debug becomes quite difficult , as single channel is split into many internal chains.
Bypass mode pattarens are kept ready before the silicon arrives, In case of any failure on silicon, bypass patterns will be used to identify the root cause of failure