The convert notes AppleScript command does work for me.  And nothing really 
changed. Are you sure the file does have these types of notes?

The highlightNote should be a list, I think, and it looks rather convoluted. 
Also did you set the myFile and skimNotes variables properly?

Does the Convert Note action work in the app?

Christiaan

> On 28 Jan 2018, at 18:37, Jan David Hauck <[email protected]> wrote:
> 
> Sorry, I didn't provide the full script, but I do set numberOfNotes.  This is 
> the full script.  It had been working flawlessly before.  
> 
> 
> tell application "Skim"
>       launch
>       open myFile
>       set theDocument to document 1
>       convert notes theDocument
>       
>       set noteTypeStrings to {"Box", "Underline", "Freehand"}
>       set noteTypes to {}
>       repeat with noteTypeString in noteTypeStrings
>               set noteTypeString to contents of noteTypeString
>               else if noteTypeString is "Box" then
>                       set end of noteTypes to box note
>               else if noteTypeString is "Underline" then
>                       set end of noteTypes to underline note
>               else if noteTypeString is "Freehand" then
>                       set end of noteTypes to freehand note
>               end if
>       end repeat
>       set highlightNote to highlight note
>       set lineNote to noteTypes
>       set highlightColor to {63798, 59381, 37996} -- New Yellow 
>       set linesColor to {45073, 3851, 6345} -- Dark Red
>       set numberOfNotes to 0
>       tell contents of theDocument
>               repeat with aNote in (get notes)
>                       set aNote to contents of aNote
>                       set theType to get type of aNote
>                       if highlightNote contains theType then
>                               set color of aNote to highlightColor
>                               set numberOfNotes to numberOfNotes + 1
>                       else if lineNote contains theType then
>                               set color of aNote to linesColor
>                               set numberOfNotes to numberOfNotes + 1
>                       end if
>               end repeat
>       end tell
> 
>       if numberOfNotes = 0 then
>               close theDocument saving no
>       else
>               save theDocument in skimNotes as "Skim Notes"
>               close theDocument saving no
>       end if
> end tell
> 
> 
> Jan David Hauck, Ph.D.
> Lecturer
> Department of Anthropology
> University of California, Los Angeles
> http://ucla.academia.edu/hauck <http://ucla.academia.edu/hauck>
> http://www.anthro.ucla.edu/content/jan-david-hauck 
> <http://www.anthro.ucla.edu/content/jan-david-hauck>
> 
> 
> On Sun, Jan 28, 2018 at 1:06 AM, Christiaan Hofman <[email protected] 
> <mailto:[email protected]>> wrote:
> You never seem to assign the numberOfNotes variable in your script. 
> 
> Christiaan

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