When you retypeset a score using a tool like Lilypond or MusicXML, it's a good idea to not only upload the resulting PDF, but the source file used to generate the score. This can be best accomplished by adding an attachment to your PDF. This way if someone finds an error in your typeset, they can easily download the PDF, extract the source, make an edit, recompile and upload back to IMSLP.
There is a good free tool called pdftk that will let you manipulate PDF files from the command line. Here's an example of how to work with a Lilypond file.
Step 1, compile your source file, score.ly
> lilypond score.ly
Step 2, attach the source, score.ly, to the generated PDF, score.pdf
> pdftk score.pdf attach_files score.ly output annotated_score.pdf
Step 3, upload annotated_score.pdf to IMSLP
Sibelius, Finale, et al.
If you are using a program like Sibelius or Finale, it would be a very similar process.
Step 1, export your score as a PDF (score.pdf)
Step 2, export your score as MusicXML (score.mxl)
Step 3, attach the MusicXML file to your PDF
> pdftk score.pdf attach_files score.mxl output annotated_score.pdf
Step 4, upload annotated_score.pdf to IMSLP
That's all there is to it.