If page numbering depends on the plug in that likely needs remade.
I don't know if exporting as idml would help or not. Have you contacted the plug in maker?
I tried to mark your answer as correct because it worked. I hesitated to contact the company which had set up the xml application because we had ended our relationship but I, on your advice, I did anyway. They were very nice, sent me the plugins with instructions how to install and it fixed everything. Unfortunately, when I tried to mark your answer no selections were available to me.
Good result. Glad they were able to help you. No worries about the answer thingie.