I have made several music projects and kept their files and all has been ok.
However recently I started making new projects from a custom template which I was told would save me time.
Now when I open up any of the projects to play the files to add things or extend on them my other projects that were once fine in
Cubase play half the song which was previously complete with no vocals and reports I have have missing files and I never moved or deleted anything.
Now all I have are incomplete songs with missing files labelled with numbers and the template name I made and changed to
name the project. All stuffed. Why do I have this issue I am meticulous and tidy?
1st post. WELCOME! 
You probably created your template incorrectly by creating the template directly from an existing project without performing a “backup project” first.
When you create a template like this the audio pool will be shared among all projects created with that template. When this happens it is very possible that audio files from different projects will get overwritten by audio files created by files recorded in the last worked project created with that template. You also end up with one very large shared audio pool where audio files can get referenced to the wrong projects. Very confusing indeed!
Because of this confusing situation I posted a feature request to improve the “save as template” function.
My initial post in the link I listed below explains my concern and proper way to create a template so you don’t end up with a shared audio pool. Take a look at that topic and see if this happened to you and for the methods to correctly create a template. If this did happen, project audio files that once referenced to the correct project may have changed. This may be fixed but, it will be a PIA for sure. Or… you may have deleted/overwritten and actually lost some audio files used in different projects. These files may only be recoverable if you were performing computer backups on a regular basis. I hope you can recover your files but… it’s probably not going to happen. Sorry.
https://www.steinberg.net/forums/viewtopic.php?f=285&t=147399
Also… once you properly create your template(s) and start using them, make sure that you have the “Prompt for Project Location” enabled when creating new projects from the Steinberg Hub. With that option enabled you would browse to your location and click on the “add Folder” button to create a new separate folder for each project.
Also… for best assist it is a good idea for you to add your computer/software/hardware specs to your forum signature.
Regards. 
Prock, are you sure that files could be overwritten? It seems that Cubase is pretty good at just incrementing existing files. I would find out which folder is accumulating all the new project files first and then show Cubase where they are at the alert on project startup. If it can load them, then its just a simple matter of using Back Up to consolidate (copy) the Project all into a new folder without much fuss.
What I am sure about is this…
When you have an audio pool that contains a bunch of audio files (maybe 100s or 1000s of files) that are used in different projects it is very easy to get confused and delete/rename/edit… or even overwrite the wrong file.
Cubase itself won’t overwrite a file but a user could very easily do it just by simply renaming a file by mistake during an editing session on a currently working project.
Cubase will even warn you that you are about to rename a file used in a different project but… sh** happens quickly while editing and once you hit the wrong button… boom, the damage is done.
Your method to recover projects with their own files is a good one but… it still is not easy. Especially for a newer Cubase user.
Bottom line… I believe it to be best practice to make sure all projects are saved to their own folder and have their own audio pool.
Regards.
True. But this is an easy mistake to make when you are a new user and I just wanted to assure rollthedice that everything might be fine. I actually think the solution is quite easy. Once you show (locate) Cubase the folder, it does the rest. At the Prompt, Locate, Back up to new folder. 
Even if you have made edits your project will know which files they are and shouldn’t have overwritten files from other projects.
Cheers
Cool. I hope ”rollthedice” tries it and all turns out well.
Regards.