It's possible to protect documents against Copy & Paste, using a
font mangling technique. It was first suggested here.
http://spivey.oriel.ox.ac.uk/corner/Obfuscated_PDF
Your problem is just a "regular" problem with PDF, rather than
the willful damage ("protection") afforded by some tool flows.
I repaired such an Obfuscated document, just to see if it could
be done, and it took two weeks of scripting and experiments to do it,
and get the resulting document close to original form (so when
you copy and pasted, the text matched what was on the screen).
XPDF was indispensable, as was a font editing program (to repair
each font table). Even with OCR to fix the font tables, I doubt
such a repair could be completely automated. So if you want
a purposefully obfuscated document fixed, it's a *lot* of work.
*******
As to the nature of your problem, fi and fl are ligatures.
http://en.wikipedia.org/wiki/Typographic_ligature
That article even has examples of your two character sequences.
http://en.wikipedia.org/wiki/File:Ligature_drawing.svg
The fix is pretty simple. Just a matter of recognizing the
Unicode for those things, and translating it back to text.
Try copy and paste in a word processing environment, to
see if that's a more compliant transport, than pasting
into Notepad. Then do a "find and replace", using the
ligature character for the find, and "fi" for the replace etc.
That will translate the one 16 bit character, into two 8 bit
characters.
Further down the page in the ligature article, they have
the mapping...
fi ligature = U+FB01
fl ligature = U+FB02
I wonder if pasting into a hex editor would work ? Then,
translate FB01 hex, into the hex for the appropriate
two ASCII characters.
I love projects like this. That's what makes computers fun.
Having to do all the work manually :-)
Have fun,
Paul