I left the magnets in place while removing filter and while cutting it open.
There might be a trace of something on the inside of filter but I'm letting the residual oil drain down to take a closer look at it later. All I can say for sure is I can tell from looking at the inside of filter canister where the magnets are on the outside.
One thing to note though - the flow of oil thru the filter is from the outside to the inside, so I think even if the magnets were not there that oil would have to pass thru the filter media before going back to the motor so the filter would probably catch most of it anyhow. Another observation - unless you have a strong magnet that encircles the filter, there is a lot of oil that would go thru the filter that wouldn't be close enough to the magnet such that the magnet could work.
Lastly, I've cut open quite a few Fram filters and even though they have cardboard end caps on the ones I've opened, they were all in place and there was no separation of the filter media.