I created an application using Web AppBuilder Developer's Edition. The app was deployed onto the companies web server (SDE) and then added to AGOL using the Create + -> An Application.
What is the best way to update the application in the future? I will be leaving this application behind and want to know the best workflow to leave in my documentation for the people responsible for updating it.
In that case then all the updates to the apps configuration will happen manually (directly editing the json files) on the web server. The other option is for them to have WAB Dev and import the app to make changes.
When you login to AGOL Assistant you have the "I want to...", choose "View an item's JSON", then find the WAB app in the right pane and select it, in the left pane scroll down to the data section (it is right under the description pane). There you will find the apps main config.json that you can click on the edit button in this panes header and now you can edit the json and save your changes.
OK let me go back an review your original post (because I made some assumptions).
The app was deployed onto the companies web server (SDE) and then added to AGOL using the Create + -> An Application.
Correct me if any of the steps below are not correct.
So you created a WAB Application using WAB Dev.
You then exported the app so that you had a zip file of the app
You extracted that zipped app to a web server "The app was deployed onto the companies web server (SDE)" Not sure why you say SDE unless the SDE server is also the web server.
You then took that url for the app and added it to the companies AGOL content using Add Item?.. You said Create > App...?