Remove the remjet before you develop the film. It won't hurt your tank at all. Just rinse a few times before you start developing if you are concerned about getting remjet in your processor or if you are concerned with carryover. There are lots of formulae for removing remjet, but just use Kodak's. It is in the pdf they have explaining ECN-2.
If I am not mistaken, remjet is just carbon. The biggest issue is making sure it doesn't stick to the emulsion on your film. I doubt it would stick to the reels, but they are easily cleaned.
I've removed remjet before on Super 8. I just balled it up and threw it into the JOBO. Didn't have any issues with the remjet. It came right off after a soak and some shakes...
Not an expert, but I hope that helps you.