now you can change also the bundle id

sign.sh

@@ -3,6 +3,7 @@ SOURCEIPA="$1"
 DEVELOPER="$2"
 MOBILEPROV="$3"
 TARGET="$4"
+BUNDLE="$5"
 
 unzip -qo "$SOURCEIPA" -d extracted
 
@@ -10,8 +11,12 @@ APPLICATION=$(ls extracted/Payload/)
 
 cp "$MOBILEPROV" "extracted/Payload/$APPLICATION/embedded.mobileprovision"
 
-echo "Resigning with certificate: $DEVELOPER" >&2
+echo "Resigning with certificate: $DEVELOPER"
 find -d extracted  \( -name "*.app" -o -name "*.appex" -o -name "*.framework" -o -name "*.dylib" \) > directories.txt
+if [ "$BUNDLE" != 'null.null' ]; then
+   echo "Changing BundleID with : $BUNDLE"
+   /usr/libexec/PlistBuddy -c "Set:CFBundleIdentifier $BUNDLE" "extracted/Payload/$APPLICATION/Info.plist"
+fi
 security cms -D -i "extracted/Payload/$APPLICATION/embedded.mobileprovision" > t_entitlements_full.plist
 /usr/libexec/PlistBuddy -x -c 'Print:Entitlements' t_entitlements_full.plist > t_entitlements.plist
 #/usr/libexec/PlistBuddy -c 'Print:application-identifier' t_entitlements.plist > t_entitlements_application-identifier   #save developer application-identifier to file

signall.sh

@@ -6,6 +6,8 @@ ipadestfolder="/Users/admin/Desktop/signed/"
 developer1="iPhone Developer: xxxx (xxxx)"
 mobileprovision1="/Users/admin/Desktop/mobileprovision"
 
+bundleid="null.null" #use null.null if you want to use the default app bundleid
+
 
 cd $ipasourcefolder
 find -d . -type f -name "*.ipa"> files.txt
@@ -15,7 +17,6 @@ while IFS='' read -r line || [[ -n "$line" ]]; do
 	#_dev1_______
 	output=$ipadestfolder$filename
 	output+="_signed_dev1.ipa"
-	"$signscript" "$line" "$developer1" "$mobileprovision1" "$output"
-
+	"$signscript" "$line" "$developer1" "$mobileprovision1" "$output" "$bundleid"
 done < files.txt
 rm files.txt