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From the sound of it the cylinder is a primatic type where the primary or heating circuit is fed from the cold water tank through a device inside the cylinder which allows water to enter the heating system but maintains the separation between the two. You can get problems with heating and hot water systems mixing if the heating side gets too hot and you get boiling which forces water past the internal air gap.
If you are just capping off the primaries at the cylinder there should be no problem.
If you are just capping off the primaries at the cylinder there should be no problem.