I doubt this is a session timeout, sounds more like the VPN is dropping.
Check the VPN status next time you get an issue.
With the port timeout setting, you can change the global setting, which affects all ports, but wouldnt recommend this is a long term, but just to prove it you could try it. But i really doubt thats the issue, as this timeout is when an existing TCP SESSION goes inactive, which apps shouldn' t do with tcp anyway. and even if they did, they should just reconnect anyway.
Sounds more like the vpn is going down and its taking a number of seconds to come back up again which is causing the timeout.
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