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If the ROS(Registry Ordering Supplement of the CFF table is not defined or using the OTF fonts defined in Adobe-KR-9, if you create a work in indesign and export it to PDF, two problems arise.
As a temporary workaround, we have confirmed that the above two problems do not occur because the ROS (Registry Ordering Supplement) of the CFF table is defined as Adobe Korea1-2.
But I think this is not a complete solution.
Adobe-KR-9 is a new set of Korean glyphs released in July 2018, and I want to correctly define the ROS of fonts created with it.
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About Problem #1, I suspect that there are two issues going on. Now that I have access to the fonts in question and the InDesign file, I am able to investigate.
The first issue is that the InDesign file is way too long. It is an entire 212-page book with front matter, six chapters, and back matter. InDesign can start behaving oddly when the number of pages exceeds 100 or greater. The content should therefore be split up into individual files, such as one for the front matter, six for the six chapters, and one for the back matter. A book file can then be created to tie them together. A single 212-page PDF can still be exported. While I cannot guarantee that this will fix the issue, there is a non-zero chance that it will. Independent of this particular problem, using a book file is considered good practice.
The second issue is that if you are developing a font with the same name in different formats, such as name- and CID-keyed, or CID-keyed with a different ROS (Adobe-Korea1-2 and Adobe-KR-9), the app's font cache file needs to be deleted. For example, if you swap the font with one of a different format, the InDesign app should be closed, then the font cache file removed. On macOS, I execute the command line "rm ~/Library/Caches/Adobe\ InDesign/*/*/TypeSupport/AdobeFnt_OSFonts.lst" in the Terminal app to remove InDesign's font cache file.
When I properly remove the font cache file, the exported PDF using the name-keyed font still exhibits the overlapping phantom-glyph problem, along with the a similar problem on four other pages (the phantom glyph is inserted, and pushes out the line on the right margin by one character). The exported PDFs using the Adobe-Korea1-2 and Adobe-KR-9 fonts do not exhibit the problem.
About Problem #2, you can try copying the Adobe-KR-UCS2 ToUnicode mapping file into the "/Applications/Adobe\ Acrobat\ DC/Adobe\ Acrobat.app/Contents/Resources/Resource/CMap/" folder, though I suspect that it won't make any difference, because InDesign-exported PDFs include an embedded ToUnicode mapping table that takes precedence over Acrobat's ToUnicode mapping file for the same ROS. However, I suspect that not deleting InDesign's font cache file may have resulted in a PDF with issues, so this should be tried again with a freshly-exported PDF following the delete-the-font-cache advice above. With that said, editing the content of a PDF file is not recommended, especially if you have access to the original authoring document.