It may be that the chimney stack is constructed with several flues - this is typical in older properties - for example to connect from the separate rooms upstairs and down.
Normally a conventional flue, where passed through a chimney stack is hooked up using a flue liner (flexible metal tube) all the way to the top. As long as this is passing through a separate flue way to that from the open fire, then it's fine. Presumably the smoke from the fire exits via a different pot, in which case it will be separate.
.andy
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