ADE 1.8 (I think) and later (2.0 does for sure) use ligature. When you have the letter combination such as fl you do get the ligature for fl if it is in the font. But older versions of ADE (1.72 and earlier) do not use ligatures and if you do put in the ligatures by hand, you do break searching.
So, the solution is to just put int he words as they should be without the ligatures and let the reading software deal with the ligatures or not. And to be honest, most people would know really care (or even notice) about there not being ligatures.
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