Have these variables on the file's datacard is flagged to update all configurations ?
They are not. I just tried flagging all the variable to update all and the behavior is exactly the same. Custom properties are removed from the drawing seemingly at random, except that properties assigned a value do not disappear. I thought at first this behavior might be cause by the variables being empty, but when I assigned a value to all variables (I put in a single letter for each), I still get undesired behavior.
Any variables that are updated with an empty value (cleared) in the transition get deleted completely from the drawing.custom properties. Properties set to be formatted as a date, however, seem to NEVER get deleted.
The moving of properties from custom to config specific in the model seems to be at random, or at least I can't determine a pattern. With the variables flagged as "update all configurations" on the data card, should it be adding values to config specific in the model, or just updating the custom property?
I know this is old, but I have an idea of what may be causing this issue.
Is this happening for weldment parts that have a single-body weldment inserted to make a derived part?
If this is the case, SolidWorks 2013 & up will DELETE all configuration-specific properties that the two (parent & child) have in common. I don't know if this is a bug or a failed new feature, but it is causing me many problems as well.
Have you had any luck fixing your issue with the document custom properties disapering when inserting a part inside of a weldment, that have matching properties? I currently use 2013 SP0 and have the same problem. I was hoping you had found a solution.