Whonix VM is not retaining installed files after reboot

I have made a new Whonix VM, named WhonixPrimary, i have had a problem occur twice now where I install a program and then on reboot it is no where to be found either in the file directory or when I try to launch it from the Terminal.

I seem to be having some trouble understanding why it keeps certain files but not other. If it makes a difference the two programs I downloaded and were lost were Remmina and Kleopatra. It has been extremely frustrating because I lost an encryption key I created.

I know it may seem like I may have accidentally created a disposable machine but I made a test mousepad file with some gibberish code save and upon reboot it retained the text and mousepad file. I will list the VMs stated settings below, if you could advise me on anything I could possibly change to ensure the programs are saved permanently.

Name: WhonixPrimary
Template: Whonix-ws-15 (current)
Networking: sys-whonix (current)

Under other:
No boxes are checked
and default disposable VM template is listed as : (none) (current)

Thanks for the welcome and help, I am a complete noob with Qubes. I appreciate the patience with learning the basics

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