CRIO Unable to Undeploy and return system to a good state

I am having numerous problems with my new hardware, consisting of a cRIO-9082 and a 9144 ethercat slave.  I had everything working well at one point.
Right now, I am just trying to get back to a good point by programming a simple vi on just the 9082 without the 9144 connected.  However, I am unable to undeploy the the 9144.  At the same time, nothing will work because "at least one deployed object is no longer connected to the system".  If I try to undeploy the 9144 from the "Compare Project and System" menu, then I get "LabVIEW:  (Hex 0x80DF0002) A file I/O error occurred."
Please Help.  Thanks.
Dustin

I am using labview to program the cRIO-9082, and am using the labview project manager to manage all the devices.  That is what I meant by the normal course.  I am changing the programming because that's part of the development process.  I am developing my application, and in the course of developing that application I chose to remove the 9144 from my system while I get things working on the 9082.  It really doesn't matter what my reasons for doing that are, as the cRIO is a configurable system, and is designed to accomodate changes in the configuration. 
That's all I did, and the result is what we are discussing here.  I have not changed any configuration files myself, but clearly labview does change files, and so I am making a guess that something got changed in an undesirable way.

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