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If I change (lower) server connections, seems it immediately disconnects any more than X connections, leading to some unwanted behaviour (stopping midway through group updates etc).

I'm pretty sure when I used to change it, it would just disconnect greater than X connections only after those connections had finished their current task (group update, part retrieval etc.).

I'll have to try. Header downloads shouldn't be getting interrupted.

They don't return till completed or deleted from the download list and it's only on return that the connections get closed out.