I am using a VPN (openvpn) to connect to the internet 24/7 ,I am also runnning a bit torrent client 24/7, there are times when my external VPN provider will disconnect for a few minutes, then recconect again as it has been set up to recconect automatically.

What happens during those minutes that the VPN disconnects? Do the applications connected to the internet stop too, or do these applications just carry on as normal passing all traffic through my ISP internet connexion instead of the VPN?

Example of what I see in the shell when openVPN disconnects (notice, first two lines, process killed by expiring key at 7:31:38, then restarts at 7:32:22):

----------------------------------------------------------------------
Sun Mar 9 06:33:22 2008 Control Channel: TLSv1, cipher TLSv1/SSLv3 DHE-RSA-AES2
56-SHA, 2048 bit RSA
Sun Mar 9 07:31:38 2008 TLS: tls_multi_process: killed expiring key
Sun Mar 9 07:33:22 2008 TLS: soft reset sec=0 bytes=406074373/0 pkts=914720/0
Sun Mar 9 07:33:31 2008 VERIFY OK: depth=1, /C=US/ST=OR/L=Halfway/O=VPN__LL
C/CN=VPN__LLC_CA/emailAddress=pki@*****.com
Sun Mar 9 07:33:31 2008 VERIFY OK: depth=0, /C=US/ST=OR/L=Halfway/O=VPN__LL
C/CN=server/emailAddress=pki@*****.com
Sun Mar 9 07:33:49 2008 Data Channel Encrypt: Cipher 'AES-256-CBC' initialized with 256 bit key
-----------------------------------------------------------------------

If you don't want apps to route traffic over your ISP's connection (no x there) I hope you blocked traffic that way. You can easily find out what decisions are allowed for traffic by checking your routes (route, ip) and see where traffic goes effectively by using iptables (-j LOG) rules or sniffing traffic with say tcpdump or wireshark (preferably with a BPF filter so you only log what you want to see).

I am relatevely new to Linux so I would have to learn iptables and all the other stuff you mention, if the apps get disconnected when the VPN is disconnected then it would not be necessaty for me to invest the time learning all that.

It is good to know I can apply rules to avoid routing traffic through my ISP, which I wasn't aware of, but I will only get into that once I find out that I have to.