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On a side note, I am surprised no one else likes to keep an original of the PDF, which is not annotated or marked. I guess I'm in the minority here as well.
Sometimes I do the same. I'll keep the originals in a separate folder and save my marked up docs in a different folder. Forms especially. But it's a conscious decision.
 
On a side note, I am surprised no one else likes to keep an original of the PDF, which is not annotated or marked. I guess I'm in the minority here as well.
I always keep the original and make a copy for annotating (GoodReader asks if you want to make a copy by default). The annoyance is when you have annotated copies on multiple apps and because of app sandboxing, you don't know which version is the most current.

Thankfully, GoodReader, PDF Expert and Windows all support Dropbox so I use that as my centralized storage to keep files in sync.

Ditto for Excel.
 
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