I am not sure if I am posting this on the right section. Also forgive my limited terminolgy.
Is it possible for the sequencing process to install the application in its original folder location?
For example, the locally installed application would install to **c:\Appfolder** and works without issue
After sequencing, the application folder location is then **C:\ProgramData\App-V\????????-????-????-????-????????????\Root\VFS\AppVPackageDrive\Appfolder**
The sequenced location will not work for the application as the **c:\Appfolder** seems to be hardcoded into other files called by the main exe. When the files that should be in **c:\Appfolder** are not found the program fails to start.
To test, I have tried copying the original locally installed folder to where it is expected to be, and the sequenced application starts successful upto a point then it fails again (probably registry and other settings are missing).
Edit: Sequencer/App-V is version 5.1
Short answer, I'm afraid you cannot. You need to fix your application to use a relative path instead of a full hardcoded path.
To understand why you can't you need to understand how the app-v client works. Checkout the video, it's short and gives you a quick introduction of the app-v container.