You can automate the (re-) opening of paths in Ai. Ai path items have a closed property. You could control that with a little JavaScript.
Does it have to be Ai/InD? There used to be a special engraving software that would take OTFs without subroutines and with a different suffix, and it would leave out the closepath statement when interpreting the paths. Should be mentioned somewhere in the depths of the forum archives.
Edit: Here is AppleScript code that opens every selected path in Adobe Illustrator. Feel free to adapt it to your needs. I guess that something similar is possible in InDesign:
tell application "Adobe Illustrator"
tell document 1 -- frontmost document
set numberOfPaths to count path items
repeat with i from 1 to numberOfPaths
set thisPathItem to path item i
if selected of thisPathItem then
set closed of thisPathItem to false
end if
end repeat
end tell
end tell