First off I would like to say that filters do just that -- filter out stuff --. They do it by having wee little holes, pores, or spaces in the filter media that allows the fluid to pass but not the solids. Filters are graded by how uniformly they trap particles. There are 2 numbers that tell how well a filter works, the beta number and the particle size. The beta is a probability that a particle of a certain size will be captured in the filter. A filter rated at 2 microns with a beta of .9 is going to trap 90% of all 2 micron particles. The beta number approaches 1.0000 very quickly for particles greater in size than the rated ones. Engine oil filters are designed to trap most particles in the 15-20 micron range. About 1/2 to 3/4 mil for you inch types. Any smaller and the filter would have too much pressure drop from in to out.
Odd thing about filters is that as they capture more particles, the spaces get smaller and they become MORE effective at trapping particles. The pressure drop across the filters will increase as this happens. When a set pressure across the filter is reached, there is a spring in the filter that gets compressed and allows the oil to flow around the filter media and go directly from pump to engine. (By the way, this happens every time you start a cold engine, if it didn't the filter media could blow out.) On modern engines, the filters almost never get to the point of clogging up -- unless maintenance has been ignored completely. Usually not changing the air filter or using a damaged air filter. Your tractor has a 2 element air filter with the housing engineered to spin off most of the big particles IIRC. Very good design.
On diesel engines the oil turns dark quickly. That is due to the presence of carbon particles or "soot" from the incomplete burning of the fuel. These particles are soft, easily stay in suspension but are so small that they pass thru the filters. You can filter them out with a by-pass filter (Amsoil sells them, others do too.)
Keeping the filter won't cause it to suddenly start spewing out a load of particles that instantly destroy the engine. It won't suddenly go into bypass mode and allow unfiltered oil free reign in the engine. In fact it will probably filter better (more smaller particles captured) and the lower viscosity oil will have a lower pressure drop moving you farther away from the point of bypass.
jb
(With all that said, I would change the filter. It's just a good habit to have, even if it is not needed.)