Firstly, if you do not use QIP or JC, then yes, you can remove those lines. If in fact, you DO use them, but as you say, the versions do not match what you are using (ie you are using more current versions), you should leave them in. Current versions of QIP (6.5A-6.7A) still use V6.2A tables - they have not changed. This is also true of JC65A - the tables have not changed for this product since V61A. You CAN remove the lines referring to QI61C though.

Re: Autodisconnect
I do not think you have to worry about this as far as QR is concerned. This would likely have more to do with your ACCPAC WSM and/or settings in the properties of the Desktop Icon or however you start it up than any one particular module running under the WSM Start List.

Hope this helps
Regards,