Hi Martin,
i can just repeat what you actually mentioned in your first post. SAPUI5/HTML5 is definitely the wrong choice for this kind of application.
1. You can't directly access a RDMS of a web application. The browser-internal Web SQL Database is no real substitute to your MS SQL server. It has considerably less functionality and is not made to save critical business data. Other storage options like HTML5 Local/Session Storage API also don't solve this problem.
2. Doing file operations from client-side JavaScript is not allowed by design. And turning off the security features of the browser, especially in production, is not recommended. I can't imagine, that the IT-security/ administrative audit of your client will accept this.
3/4. That also won't work with JavaScript. You could create a web service(oData) wrapper around your .NET logic and call them from your SAPUI5 app. Because your client wants 100% offline support, you need to host these services. Locally! Please don't do that...
5. And no, Cordova won't solve your problems. Cordova is designed for mobile devices/OS (Android, iOS etc.) and not for your use case.
Listen Martin: It's really, really a bad idea to replace your existing .NET application with a web based one. The current and upcoming offline functionalities of JavaScript are not designed to meet your business requirements. The browser is a sandbox. And local entities outside this sandbox (your .NET libraries, local RDMS, filesystem, camera SDK) can't be accessed. Developing a native application with .NET or Java is the better approach.
Besides, your current .NET technology stack (C#, WPF, MVVM pattern) sounds very appropriate to me. An ideal architecture for your use case 
Regards
Michael