fuel from tank to fuel pump, to fuel filters, to injection pump, then to injectors. Excess fuel returns to tank via return line at last cylinder. Injection pump may also have return line connected to return via Y fitting or may return to tank directly. Trace return line from top of tank to see where it ends up at engine
Returning to filter is not the original design and is a change done by some PO. There are zero air bubbles in supply and return, you would notice very erratic engine operation if so. I would restore to original design.
If engine runs fine there is no damage to injection pump. Make sure the fill plug is cracked open or nothing will drain. Stick a piece of wire in the middle plug to make sure it is dry. Just add oil and check frequently. If your positive there is no oil, then it could be a seal. Not a trivial replacement.