Keep mesh prepared when an extraction matrix has us create new NodeElems

[roystgnr]

I can work around this at the application level, but we shouldn't have to.

[moosebuild]

Job Coverage on 783dbf3 wanted to post the following:

Coverage

	a1fef2	#3844 783dbf
	Total	Total	+/-	New
Rate	62.68%	62.00%	-0.68%	100.00%
Hits	69089	68345	-744	10
Misses	41140	41890	+750	0

Diff coverage report

Full coverage report

This comment will be updated on new commits.

[roystgnr]

Closing this in favor of a much bigger branch with diagnostics and fixes for the bugs I uncovered.