There are about 25 layers that I turn on for each page in ID, so I can't save it as a flattened PDF (unless I am missing something). Each layer = a page.
Hi @displaced7 , When you Save As PDF/X-4 check Create Acobat layers...

Then in InDesign Object Layer Options will be available:

A few thing to watchout for with PDF/X-4, you won’t be able to Edit Original, so you’ll need to keep an editable version as .AI. For me that’s a non starter, but in your case it could be a fix because the placed images are going to get compressed and embedded in the PDF, which might fix any file corruption.
Also the default PDF/X-4 preset downsamples to 300ppi, so if you scale the PDF up in ID, the Effective Res will go below 300ppi