With FoxTrot 7.2 and later, you can specify whether to use Xpdf or Spotlight’s importer, for each individual file. In the search results list, select the files that need to be re-parsed, and select “choose PDF parser” in the contextual menu. This requires having write permission to these files, to set an extended attribute.
You can also set the PDF parser to use for specific files using one the following Terminal.app commands: xattr -w com.ctmdev.foxtrot.extractor xpdf [file ...] xattr -w com.ctmdev.foxtrot.extractor spotlight [file ...] xattr -d com.ctmdev.foxtrot.extractor [file ...]