Which files are transferred when using Transfer purchases from? iTunes is still very confusing to me, and today I tried to upload a book on an iPad.

After adding one pdf file to the iBooks library on OS X, I tried to sync the iPad. Unfortunately, iTunes insist on erasing everything before synchronising the content, because it's not using the same iTunes library. Apparently, iTunes refuse to simply upload a file to the iPad. 

At that point, I thought I could just transfer back the selection of books (not bought through any store, really just PDF files that happen to be on that iPad) and manually add them together with the new file I wanted originally. I have never been able to get the files back. It looks like Transfer purchases from ignore those files. (ITunes / Files / Devices / Transfer purchases from )

So I ended erasing the content of iBooks on the iPad to put a new file.
Am I missing something, or is iTunes just developed with frustration in mind ?
You are right about iTunes showing great signs of strain. It was designed for a pretty simple task that now overwhelms it with too many functions - it's very un-Mac like due to how long it has taken Apple to kill it and reinvent all the jobs it does with better tools.

Now - transferring purchases was really simple in iOS 7 and earlier. There was no family sharing, there was no app thinning, there was no just in time downloadable resources, iBooks wasn't a separate app that can complicate things.

I'll try to explain how to make use of the tools, but you will probably spend some time trying things out and changing your workflow to accommodate the tradeoffs that were made in designing iOS and iTunes.


Each class of data has a "sync source" so you could for instance, sync iBooks from Mac A, Apps from PC B and songs from Mac C. You are right that iTunes is designed to wipe old content from a previous sync source before switching to a new source. You can usually transfer or back things up, accept the wipe and then proceed, but I've seen cases where you literally have to go get things again in this case. Especially when you don't sync with multiple computers and instead software bug resulted in the system thinking the same iTunes was a different iTunes.
You can get around this a little with a good backup - but pay attention to iCloud settings since if you skip backing up some things, you still have to re-download them.