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It is not a good idea editting sections in notepad. If you want XPATH change through this mode, in addition to 'replace' action you will need to find the length of the XPATH you are going to replace. This information also you need to update accordingly in the line in which your XPATH is being replaced. Else when you check-in the FAP back to library, Studio will read only upto the length of previous XPATH.
e.g: Length of below XPATH is 106
Hope you are considering XDD concept in such scenarios.
Although I'm not sure I would recommend using Notepad to search and replace text, I'm not sure that is the problem. I would suspect that you may have fallen prey to word-wrapping in Notepad and that is why the subsequent use of the FAPs was unsuccessful. You would need to use a tool that does not rewrap the lines when loading or replacing the text.
Next, your situation is one that points out the value of using the Extract dictionary (XDD) file. If all your mappings were defined there, then there would only be one file to change (or maybe a few depending upon need) rather than thousands of FAPs to change.