Does making your web map an application on ArGIS online cause loss of auto updating for the layers in the web app?
If I have understood your question: You want to know if creating a Web Application in AGOL interrupts features being updated in the original Web Map?
If that is the case, no. The web app should not interrupt the auto-updates you have running in the web map.
The Web App is like a viewer for the web map, so as long as the web map is live and well then your Web App will display / act as you planned it to.
If you allow your Web App to edit features that are being auto-updated, then that is a different story and there might be some conflicts in the edits.
The way I have created web apps involves creating a blank Web App using a template or from scratch and then reading the contents of the web map into the web app.