Missing glyphs square boxes that have an X in it

Hi gang,

File this question under "I thought I should know this by now" but I really don't:

I made an InDesign layout, exported a PDF, then three years later on couldn't find the .indd project. 

Needing to update the PDF layout, I recreated the layout quickly in a new ID file.

I opened the old existing PDF file in Acrobat and exported the text out as a Word docx file.

I placed the word docx file back into the new ID layout.

The problem: In places in the text where font glyph arrow characters are used, it comes in with missing glyph squares (that have an X in the square). 

It seems to be a closed loop, so why am I getting missing glyph Xsquares?

I tried running Peter Kahrel's unicode fixer script, and that fixed them, but why did it occur at all?