So, I rebuilt the file. I created a new one from scratch and moved in all of the elements per each layer. I also went into each of the native Illustrator files (yes, they were placed into inDesign as .ai files) and stripped out any unused color swatches and patterns.

Then, I tried to export the pdf with the Transparency Flattener and it worked this time. Few things happened though. It created a 1.35gb file! and Acrobat Pro is having issues “reading” the file. I am sending it off to the printer as is to see if they can work with it. If not, I am also “packaging” the file for output (old skool)

InDesign/Adobe really has to offer a better solution for this don’t you think?

Is it possible to create a normal Hi Res pdf from the InDesign file and then, after it’s been generated, strip the fonts from the document or flatten them in Acrobat?

Yes. If I try to export a normal, hi res/lo res pdf, there is no problem. But as I am starting to look and wonder at what’s going on, I am starting to wonder if it is just taking longer to create the pdf. The 0 Bytes file is just in place because InDesign is building the file and it’s not “cooked all the way” yet. It is really odd that it would take so long, but there is a panel called background tasks that I opened up in InDesign. It is showing a very SLOW progression for the file. I am wondering if that is what’s going on?