To be clear, it doesn't look like you're actually stopping the DAQ Assistant tasks - if you right click on them and click Open Front Panel you can see their block diagrams (or perhaps equivalent block diagrams). If you want to go back to DAQ Assist, you can just close the new window (Defer Saving) and use Undo - you'll get a message asking if you want to save or not the new VI, click Don't Save.
They're 'Preallocated Reentrant Clones', so one shouldn't mess up the other. Some quick testing suggests they also don't mind being called in multiple For iterations within a While loop (as Altenbach already pointed out - it's not so easy to work out what's what when While loops are green...) but I didn't try with Sequence structures.
What do you mean by "appears to be stopped based on the while loop upstream in the sequence"?