Internal Flue Sealing

We've just moved into a house with an Ideal Atlantic Combi 24 gas boiler. One of our first moves was to get a smart meter fitted, and the engineer who came to do this immediately slapped a 'Do Not Use' notice on the boiler as the flue hadn't been sealed internally. He suggested using fire cement to do this. As the installation was under guarantee I called the plumber who fitted it to do the fix. He came round quickly, and sealed the flue using clear silicone sealant. We want some other plumbing work doing, but I'm not sure about the competence of this guy. Is silicone sealant OK for an internal flue seal on this type of boiler? It seems to be working OK for hot water, but I don't want to have problems in the winter when we turn the heating on.