They are the Data and Resource forks - also known as A and B trees. Every file or folder is contained as a single entry on the drive. A little history makes this easier to understand. So whether they merge or not depends on the location of the second file icon when you let go of your mouse or trackpad button.It sounds like most of what you're describing are the AppleDouble files, which are created on DOS/Windows formatted drives by the Mac OS. If you drag the second document above or below the thumbnail of the first document then the two documents will not merge.

If you drag the second document onto the thumbnail of the first document then this will cause the two documents to merge. To force them to merge, you need to open the thumbnail window of the first PDF document (‘View’ then ‘Thumbnails’ from the menubar), and then drag the icon of the second document onto the thumbnail of the first document. If you click on both documents together in the finder it will open them as two separate documents. If you just use the ‘Open’ menu from within preview it will open them as two separate documents. You may be wondering how to force the documents to merge when you open them in Preview. How to force 2 documents to merge when you open them in Preview If the files have not merged in preview, you can merge them by printing them to PDF. In this description it will tell you whether there are one or two documents open. After this title there is a short description in brackets. If you open two documents in preview then have a look at the top of your preview window there is a title with the name of the document. Here’s how to tell if they have merged or not. If they are merged then all you need to do is save, but if they have not merged then you need to print them to a new PDF file. When you open 2 or more PDF documents in preview, depending on how you open them, preview will merge them together into one document OR it can open them as two separate documents. You can open them as seperate documents in Preview and drag pages from one to the other. You can open them as seperate documents in Preview then merge them by printing them to one pdf file. You can merge them into 1 document in Preview as you are opening them.

As with previous versions of OS X, there are 3 different ways that you can do this.

Apple have retained the ability to merge two PDF files with the built in ‘preview’ app in OSX El Capitan.

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