Using an XML file to control the behaviour of the Creo Illustrate file is a powerful tool. You can create Figures automatically, define what parts should have a callout, etc. The problem is that this file is only taken into consideration when the source file (PVZ, .ASM, STEP, etc.) is imported. If the XML file is updated, (e.g. add a figure, redefine what parts should have a callout, etc.) the changes are not taken into consideration. This will be a powerful tool if you're working with sBOMs in Windchill where you can automate the creation/update of the XML file from the sBOM.
Steps to reproduce the problem
Create a .pvz file from e.g. an .asm file and call it e.g. 1000.pvz.
Create a another .pvz file from the modified .asm file (e.g. remove a part) and give it the same ole name (1000.pvz). Store it in another folder than the first .pvz file.
Import the first .pvz file and create a new figure in Illustrate, add some call outs, etc. and save the .c3di file in the same folder as the original .pvz file
Go to Tools ==> Edit Structure and export the BOM, call it the same as the .pvz file (1000.xml)
Modify the .xml file in the Figures tag by e.g. removing an item, see below: