@ARTICLE{ FormatInQuestion,
   author = {XXX},
    title = {YYY},
}

bibtool --preserve.key.case=on --preserve.keys=on refs.bib > refs_new.bib

@article{ doi:10.1016/s0012-365x(97)00126-x,
_________________________________^
*** BibTool ERROR:  (line 2101 in ./references.bib): Unexpected character encountered

Stuff after "}"---line 2 of file bibstump.aux
 : citation{b{ra
 :               }ces}
I'm skipping whatever remains of this command

@article{quo"tes,
  author={A B},
  title={T},
  journal={J},
  year=2000,
}
@article{(paren),
  author={A B},
  title={T},
  journal={J},
  year=2000,
}
@article{o@th[;]er,
  author={A B},
  title={T},
  journal={J},
  year=2000,
}

begin{thebibliography}{1}

bibitem{quo"tes}
A~B.
newblock T.
newblock {em J}, 2000.

bibitem{(paren)}
A~B.
newblock T.
newblock {em J}, 2000.

bibitem{o@th[;]er}
A~B.
newblock T.
newblock {em J}, 2000.

end{thebibliography}

@article{quo"tes,
_____________^
*** BibTool ERROR:  (line 1 in ./bibstump.bib): Unexpected character encountered

*** BibTool WARNING: Skipping to next '@'

*** BibTool WARNING:  (line 7 in ./bibstump.bib): 49 non-space characters ignored.

@article{(paren),
________________^
*** BibTool ERROR:  (line 7 in ./bibstump.bib): Unexpected character encountered

*** BibTool WARNING: Skipping to next '@'

*** BibTool WARNING:  (line 13 in ./bibstump.bib): 46 non-space characters ignored.