1. Other Problem Fonts
A Type3 font is a special case where the “glyph” is commonly a logo or barcode which makes it extremely difficult to know which unicode to enter in the Characters Editor. In this case, one special trick you can employ is to literally place the original PDF (by using InDesign’s File:Place… menu item and choosing the specific page number when importing) at the desired location on the page and then crop the picture box so that just the logo or barcode area of the PDF is viewable. Or you can edit the PDF in another application, such as Adobe Acrobat, Adobe Illustrator or Adobe Photoshop, by deleting unwanted pages and removing all of the other objects on the page, leaving just the logo or barcode, then save to a new PDF and place it in the document at the proper location.
2. Encrypted PDFs
Secured or encrypted PDFs which require entering a password to be able to convert, sometimes use “scrambled” definitions of unicode values to prevent copying the text. Unfortunately, there isn’t an easy way to convert the characters short of converting each page to a TIFF image and then using advanced OCR (Optical Character Recognition) to extract the text stories.