Have you ever tried to merge a few files and ended up with missing characters on some of your pages in the resulting PDF file? Here is a description of one of these instances – as a question posted on Acobatusers.com: https://answers.acrobatusers.com/text-missing-combining-q134046.aspx
I’ve never seen this problem first hand, and therefore was not able to find a workaround that would fix it. I’ve asked for sample files for many years, but never got anything useful. I finally struck gold and received a couple of files that show this problem.
Once I had access to a file that had missing characters, I tried a number of different things. I’ve always suggested to un-embed fonts, so that was the first thing I tried. You can un-embed fonts using the PDF Optimizer (File>Save as Other>Optimized PDF…) in Adobe Acrobat XI Pro (unfortunately, the ‘Standard’ version does not have this feature). When you bring up the optimizer, you can configure different categories. I unselected all of them with the exception of “Fonts”, and then selected to un-embed all fonts. Acrobat crashed. It crashed on both Windows and the Mac. So much for the workaround I had suggested in the past…
After a few more unsuccessful attempts, I ended up with a process that works – at least for the files that I had access to. Here are the steps you need to take:
Open the file in Acrobat XI Pro. I assume you have the merge result, so some characters will be missing:
The first thing we need to do is to split the document into it’s individual pages. This can be done using Tools>Pages>Split:
On the split dialog, select to split after every page:
Click on the “Output Options” and select to save the split pages in a separate directory. That will make it easier to merge these files again, once we are done. When you check the output files corresponding to pages with missing characters, you will notice that the characters are still missing.
Now that we have individual pages, we can fix the font problems. We could do this manually for each file (and if you only have two pages, that may actually be the faster method), but for many pages, it’s easier to have an Action that takes care of that.
To create an Action, select Tools>Action Wizard>Create New Action… (on the Mac, you will have to open a document to have access to this function – I always use Cmd-Shift-T to create a blank document). On the “Action Wizard” dialog, expand the “Save&Export” section and select the “Save” step. Now either double-click on Save, or use the “+” button in the middle of the dialog to move it to the right side. To specify the save options, click on “Specify Settings”:
This will display the “Output Options” dialog. Select to run the “PDF Optimizer” and click on the associated “Settings” button:
The next dialog looks like the PDF Optimizer dialog that pops up when you select File>Save as Other>Optimized PDF, so if you want to do this step manually, the same settings apply.
On the “PDF Optimizer” dialog select to retain the current PDF version (“Make compatible with”), unselect all categories but the “Fonts” category and select to “Subset all embedded fonts”:
Click on the “OK” button and provide a name for the just created PDF Optimizer configuration (e.g. “Subset embedded fonts”). Click “OK” again and then save the newly created Action under a meaningful name (e.g. “Subset embedded fonts”):
Now we can process all the individual pages we converted the original document to. On the “Action Wizard” panel click on the new Action to start it. This will allow you to select all documents to process. If there is anything listed in “Files to be processed:”, remove any existing entry (The active document will be listed if it’s a document that was already saved to disk. If you created a blank document on a Mac, that document will not be listed – unless you saved it since creating it). Click on the “Add Files” button, browse to the directory where you saved your individual pages, and select all of them. Don’t worry about the order in which the files are listed, the order in which the files are processed does not matter. Then click on the green “Start” button. This will now process all files by opening them and saving them with the settings we have specified. Once done, you should be able to verify that the missing characters are back again. BTW, the last file processed will remain open, you can close that without any problems.
All that’s left to do is to merge the files back into a single PDF file. Select File>Create>Combine Files into a Single PDF… On the dialog that gets displayed, click on the “Options” button:
Make sure that “Single PDF” and the “Large file size” are selected – as indicated in the screen shot. Click “OK” to get back to the “Combine Files” dialog. Click on the “Add Files…” button, browse to the directory with the individual PDF pages and select all of them. All files names should now be listed in the correct order. If not, you can re-arrange list list by dragging an entry to it’s correct location, or by moving items to the front or the end of the list using the arrow buttons below the list.
After clicking on the “Combine Files” button, you will get a file with the same pages as in the original file, but now without missing characters.
If your original file has bookmarks, or other interactive features, you may want to replace all pages in the original document with the pages from the just created new document. This will make sure that all interactive features are still working. You can do that by selecting Tools>Pages>Replace.
What I describe here may not work for your specific file, but give it a try and let me know in the comments what your experience is.
[Update] If you want to understand why this is happening, I wrote a long explanation about the technical background here: https://answers.acrobatusers.com/ViewQuestion.aspx?questionId=190200&#answer237469