In the PN tree you need to update to when the last clean Scintilla import was made, you can find this in the code browser:
hg update --clean [last_clean_revision]
Now swap in the latest scintilla bits:
cd third_party move scintilla c:\temp\scintilla move [new_scintilla_bits] scintilla
Now update the tree:
hg addremove scintilla hg commit -m "Add scintilla release x"
You've now created a new mercurial head revision, but want to switch back to your main one:
You'll see a list of heads, pick the real head (usually the revision previous to your scintilla commit) and switch to that:
hg update --clean 9998
Merge in the scintilla change:
hg merge 9999
Check everything still builds and fix any problems, then commit:
hg commit -m "Merged scintilla release x"