Moved to InDesign forum.
Export the file to IDML and then open that and then try to package it again.
I have created a plugin to strip missing plugin info from the documents, you can try it out at the following location
This will save you the effort to export your document to IDML and then to INDD.
Currently its available only for CC2017 MAC, let me know your thoughts on the product. You will have to Save As only once, the first time you save the document after ignoring the missing plugins using my inexutils plugin and then you are all set to go.
Suggestions for improvements are always welcome