I'm not sure I follow you.
First, if you can get it to work by just recreating the section, that might be the best thing to do. It could be useful to keep a copy of the one that doesn't work to compare it to the one that does work (i.e. use WinDiff or another tool to compare the before and after files). This is especially helpful for Microsoft to be able to fix issues if they exist.
As for a 2nd data connection, it should not affect the first.
Any field can exist in the data area or the query area. There is nothing special about those two areas -- they are just sections in the view. You can put your data or query fields anywher on the form. They are kept separate in the DOM. Visually, they can appear anywhere in the form.
Greg Collins [InfoPath MVP]