So far nothing on "Glycerine" based Hydraulic fluids. However your callout of "Submarine" operations, and a fear of possible detremental effect on seals within your filtration appratus leads me to believe you may have a "Phosphate Ester Fire Resistant Fluid" Below I have attached an excerpt on this fluid used in the U.S> Navy.
http://www.tpub.com/content/engine/14105/css/14105_39.htmPhosphate Ester Fire-Resistant Fluid
Phosphate ester fire-resistant fluid for shipboard use is covered by specification MIL- H-19457. There are certain trade names closely associated with these fluids. However, the only acceptable fluids conforming to MIL-H-19457 are the ones listed on the current Qualified Products List (QPL) 19457. These fluids will be delivered in containers marked MIL-H-19457C or a later specification revision. Phosphate ester in containers marked by a brand name without a specification identification must not be used in shipboard systems, as they may contain toxic chemicals. These fluids will burn if sufficient heat and flame are applied, but they do not support combustion. Drawbacks of phosphate ester fluids are that they will attack and loosen commonly used paints and adhesives, deteriorate many types of insulations used in electrical cables, and deteriorate many gasket and seal materials. Therefore, gaskets and seals for systems in which phosphate ester fluids are used are manufactured of specific materials. Naval Ships’ Technical Manual, chapter 262, specifies paints to be used on exterior surfaces of hydraulic systems and components in which phosphate ester fluid is used and on ship structure and decks in the immediate vicinity of this equipment. Naval Ships’ Technical Manual, chapter 078, specifies gasket and seal materials used. NAVAIR 01-1A-17 also contains a list of materials resistant to phosphate ester fluids. Trade names for phosphate ester fluids, which do not conform to MIL-H-19457 include Pydraul, Skydrol, and Fyre Safe.
Phosphate Esters by their very nature are "Organic' And as to the "Solvent" They are also capable of dissolving and destroying a large number of types of seals and gaskets.
AS an "Organic" product nad as the application is of a highly sensitive matter "Submarine Hydraulics" I would recomend if the product in question is indeed a "Phosphate Ester" replacing the product with new material instead of attempting a filtration operation to attempt to bring the product back into specifications.
Of course we are not 100% sure that the product is indeed a Phosphate Ester, but it is highly likely.
Not an exact answer, but we appear to be on the right track.