For some obscure reason (probably related to the fact that update/scripts is the folder containing install-scripts) if a folder is named scripts, it does NOT get copied in a update.
Example situation to reproduce, using the sample update in this repo:
files/install
/home/pi/coderbot/scripts/check_conn.sh
produce the update, with the script handling files doing this:
FILES=${FILES:-../files}
[ -d "${FILES}/install/" ] && cp -a ${FILES}/install/. $ROOT
No errors reported, update_status remains at done showing success.. everything else is copied correctly.