Kevin,
We don't support Paratext on this list, but I can comment on FLEx's default behavior. Searches in the lexicon browse view, and concordance view, have a check box "match diacritics". That box is unchecked by default so FLEx should ignore all diacritics and give you search results with all occurrences of the base character regardless of the diacritics. If the issue is not related to diacritics, then I would second Mike Maxwell's suggestion to use regular expressions. If you have not used them they use a powerful syntax for searching and manipulating text. The is quite a bit of information about regex in the Help.
Jeff Shrum
SIL International
Language Technology Consultant
Dallas, TX
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