This sounds like exactly the sort of thing that the Project Export functions would achieve for you.
If you have not seen that feature set I am guessing that you have Monarch Standard rather than Monarch Pro.
If you have Pro and still cannot do what you want I may have missed something important in your description so let me know and I will think again.
If it was my call I think I would seek to upgrade to obtain the functionality without the need to develop, test and support separate code but maybe the upgrade costs would be very much higher for you if you looked to follow that path.
From what I know it sounds like you are doing what you need to do. However some of the other people with requirements and constraints similar to yours may have some alternative suggestions so I will leave the floor open for them.
I have Monarch V8 Pro installed and thru visual basic load a report once and apply a model and then apply several filters and extracts whether table or summary without closing the report or model.
Check out the Monarch Programmers guide [url="http://www.datawatch.com/pdf/products/monarch/Monarch_8_Programmers_Guide.pdf"]here[/url] for more information.
If you have more questions on using vb, post back here. There are several forum members that use vb scripting and are willing to help you out.
I can't help you with your batch files as I don't use them at work but I'm sure someone knows more about than I.