The issue explained has only started occurring in the last month - June 2017. Sometimes when I have been exporting files in Indesign to PDF'S using Smallest File Size settings the size comes out as huge. For example one of the files I worked on last month I was able to export at 5mb. I opened it up and altered a few sentences, and when I re-exported on the same settings as before is now coming out as 13mb! I separated the pages in Adobe Acrobat Pro to see which page was causing it and although most pages had low memory sizes (150-250kb average) some were coming out at 3-7mb. Looking into these pages I would see that they were some (not all) of the pages with links to PDF's on them. I tried moving the problem link to different pages and re-exporting, sometimes the size coming out lower, sometimes the same as before. Whats most confusing is that I have links to the same PDF in the same document on different pages with no problems at all. Originally I would circumvent this issue by re-saving the PDF as an AI or PSD and re-linking the problem link to that file instead but now its started to have the same issue with AI and PSD files as well. Originally I've been using my own custom Smallest File size Settings but have since tried using the preset Smallest File Size settings with the same results and even had a co-worker try exporting it on their computer using different custom Smallest File Size settings but with the same results.
I'm using Adobe Indesign CC 2017 with the latest updates on windows.
Any help would be greatly appreciated.
Have you been reimporting the pdf into the same graphic frame. I have seen graphic frames themselves become corrupt in the past. Try drawing a new frame and importing the pdf (which you've said does not show the same bloated file size on other instances where it is used in the document) into a new frame.