Eliminating "bookmark" from exported/imported Google Doc?

Most of the clone or alternate word processing apps are only Word-compatible in the loosest sense; you can move their files around to any app that opens and saves in Word format, but there are often significant differences in the actual document structure, markup, encoding etc. These faults often don't show up until you pass the doc to an app that expects full Word compliance, for translation, formatting, etc.

If you aren't using Word for these purposes, it's wise to pass the document through a genuine copy of Word (open-Save As to RTF, DOC and DOCX) to clean up and organize it as much as possible. One of the three Word formats, from a genuine copy of Word, will often import more cleanly and with fewer anomalies and glitches than from "Word export" from Docs, Pages, etc.

This should work: 

app.activeDocument.bookmarks.everyItem().remove();

https://creativepro.com/how-to-install-scripts-in-indesign/