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After comparing your version of the refrigerated warehouse example file to what is provided with the EnergyPlus installation, I realized that you had also saved the IDF using the "Sorted" option with IDF Editor. I tried opening the original example file in IDF Editor and saw 3 warning messages like this:

Basically, there is a Table:IndependentVariable object in the example file with more input fields defined than what IDF Editor can read. As the error mentions, saving the file in IDF Editor will lose model data, which is what's causing the severe error you posted about.

The error also mentions checking the IDD (input data dictionary) file to review the rules for this table object type. At the end of its rules, the values can only go up to 15. There is a table object named ColmacCoilInc_IndependentVariable1 which has 18 values defined, and 4.44 is value #16.

To avoid this issue, you can either:

1. Make your changes (deleting output variables) to the original example file in a text editor instead of IDF Editor.
2. Edit the IDD file to allow more values to be set in each object type that this warning is referencing when the IDF is opened in IDF Editor. After editing and saving the IDD file, try to open the refrigerated warehouse IDF again in IDF Editor.