How far along are you on flushing the bow thruster system? I'm likely too late but I'll carry on anyway.
Normally you should not connect the actual thruster at all untill the system is cleaned. Done by using fittings to connect the two hoses together. That way the thruster never sees contaminated oil.
The control valve should be disassembled and cleaned. They are not hard to do but other wise some water or moisture may stay to cause later trouble. It can hide and stay in the lower parts of the spool and at the spool ends where there is almost no oil movement so little or NO flushing.
The tank should be completely swabbed out.
Vacuuming the lines out is a good idea
but air pressure will probably do a much better job.
Both is even better.
Just be sure the hose end is firmly contained so it cannot fly about, spraying oil everywhere and maybe smacking and damaging something.
You will want to put the end firmly into a jug like an old plastic fuel jug/jerry can so any oil is definitely contained. In addition to solid oil there will be mist. Just ensure there is a good escape hole for the pressurized air or you may burst the jug. I think an old oil container will be on the light side. The fuel jug/jerry can can then be cleaned later.
With the thruster out of line you can use a cheaper oil since no pressure, or very little will be developed. Reswab the reservoir out once flushing has been done, then refill with the correct oil. Whatever remains of the flushing oil should be so minimal that it should not cause problems. If you want to be sure then do a final flush with the final oil and then clean the tank again.
You have salt water which will be far nastier in the hydraulics than some fresh water so it must be removed. thoroughly.
And of course , as suggested, contact the mfgr about any specific instructions they have.