WARNING
Biodiesel may be incompatible with the diaphragm in your fuel pump!
You will also have to replace any remaining OEM flexible hose and O ring seals in the fuel system. Any generic parts bought in recent years *should* be biodiesel compatible.
Personally I'd just put the time into getting the fuel system absolutely tight and free of weeps. Its not rocket science - a few new seals and replacing or reconditioning anything with a damaged sealing surface should do it. You've got to do it anyway as if you are discharging oil in your bilge water, try convincing any official it's only biodiesel and should be ignored . . .
As to the on engine filter - that's your last line of defence - it should stay clean if your bulkhead mounted primary filter is doing its job, but if there is a defect in the filter membrane in the primary filter or the flex line between the primary and the engine starts to break down due to all the vibration it experiences, it it there to keep the debris out of your expensive, delicate and impossible to repair at sea injection pump. DON'T bypass it. If you cant cure it's leaking tendencies without over-tightening it, talk to a diesel injection shop about a suitable replacement with good availability of spare elements. All secondary filters for the same type and size of injection pump are more or less equivalent . . .