How should I handle an application suite with a common directory?

So.. when you open exactly an app and then you close it, you want the data to be saved in 3 different apps altogether? I think using Custom.nsh file is the only alternative I can think of. Something like this should work (not tested):

Var AppPath1
Var AppPath2

Var App1Running
Var App2Running

${SegmentPrePrimary}
	StrCpy "$AppPath1" "$PortableAppsDirectory\AppNamePortable1"
	StrCpy "$AppPath1" "$PortableAppsDirectory\AppNamePortable2"
	; We are using App3 right now, no need to store its path

	${If} ${FileExists} "$APPDATA\PublisherName\Common\*.*"
		; Other apps already running
		; Do something here if needed
	${Else}
		CopyFiles /Silent "$EXEDIR\Data\Common\*.*" "$APPDATA\PublisherName\Common"
	${EndIf}
!macroend

${SegmentPostPrimary}
	; Check if App1 still running
	${If} ${ProcessExists} "AppName1.exe"
		${GetProcessPath} "AppName1.exe" $0
		${If} $0 == "$AppPath1\App\AppName1\AppName1.exe"
			StrCpy "$App1Running" "True"
		${EndIf}
	${EndIf}

	; Copy data to App1 if not running
	${IfNot} "$App1Running" == "True"
		CopyFiles /Silent "$APPDATA\PublisherName\Common\*.*" "$AppPath1\Data\Common"
	${EndIf}

	; Check if App2 still running
	${If} ${ProcessExists} "AppName2.exe"
		${GetProcessPath} "AppName2.exe" $0
		${If} $0 == "$AppPath2\App\AppName2\AppName2.exe"
			StrCpy "$App2Running" "True"
		${EndIf}
	${EndIf}

	; Copy data to App2 if not running
	${IfNot} "$App2Running" == "True"
		CopyFiles /Silent "$APPDATA\PublisherName\Common\*.*" "$AppPath2\Data\Common"
	${EndIf}
	
	; Copy data to App3 (current app)
	CopyFiles /Silent "$APPDATA\PublisherName\Common\*.*" "$EXEDIR\Data\Common"

	; Remove data if App1 and App2 are not running
	${IfNot} "$App1Running" == "True"
	${AndIfNot} "$App2Running" == "True"
		RMDir /r "$APPDATA\PublisherName\Common"
	${EndIf}
!macroend

Don't forget to remove %APPDATA%\PublisherName\Common from [DirectoriesMove] section in AppNamePortable.ini. Good luck!