On the onChange Catalog Client Script form, there are some variables missing from the dropdown menu. On the Client Script form, the source of the variables are set to catalog item. (not variable set)
This issue could have been caused by orphaning child records of variable sets. These variable sets could have been related to the missing catalog item variables. If you notice, the 'variable set' field of the missing catalog item variable is blank, but there is some data/reference when you bring up 'show XML'. The XML on the missing catalog item variable record shows a reference to a Variable Set that does not exist.
You can fix the issue by adding the 'variable set' field to the form layout of the missing catalog item variable. Then, delete whatever is being held in the 'variable set' field even though it's blank on the surface. Alternatively, you can select any other variable set, and then set the field to blank/empty.
If multiple catalog item variables are affected, you may be able to 'set empty' the Variable Set field with a script.