I am mostly just looking for some good ideas on how to remove entrained air from oil while filling a bearing assembly.

The application is downhole oilfield tools.

Currently tools are filled with three different types of oil. Their viscosities range from 46-460 cSt @ 40 degrees celsius.

During the fill procedure, oil is pumped out of a barrel into a port on one end of the housing. The oil fills the housing and flows back out of the return line and back into the barrel. The pump used is just a standard pneumatic transfer pump. Currently oil is circulated for about tenty minutes through the housing. While one end of the assmebly itself is raised and lowered. All in an attempt to remove air.

Pressure during the fill is low for most of the procedure but at one point the return line is closed and the bearing assembly is pressured to approximately 80 psi to set a floating piston that seals the bearing assembly at one end.

I have seen some inline deaeration devices for fuel oil but the pressure ratings are too low and I am not sure how the increase in viscosity would affect their function. It would be possible to bypass the dearator for the piston setting then circulate at low pressure after.

The mental diagram I'm getting is a bit on the foggy side, so I may not have a realistic idea about what needs to be done, but what I think you need to do is vent that air somehow before circulating, preferably at one or more high points, rotating as necessary.  A vent(s), perhaps a valve, or a hex head bull plug, or something similar, while the tool is held in a position such that oil is injected low forcing air high and out, turning at times as needed.  Recirculation may be contributing to the problem. If you emulse, its too late.

First, avoid entraining air. Fill low and bleed/drain high.
Second, if there are air pockets, you may be getting air entrainment during the high pressure cycle. If so, I would do the high pressure early in the fill cycle and then flush/circulate enough to remove the oil that may have picked up air during the high pressure phase.
Use one barrel to fill and another for the return. After the tool is filled, worry about removing the possible entrained air from the return barrel.
Re; vacuum. Have you considered vacuum on the tool and then breaking the vacuum with the fill oil? Possibly a coating of oil on the outside of the shaft to aid sealing and inhibit drawing air past the seals.

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