Vagrant resets the .vagrant directory each time I use vagrant up

I found the answer to my problem, hopefully it will help others.

The issue was some VM's sitting in my C:/cygwin64/home directory, and they belonged to administrator, they could also only be seen on Oracles VirtualBox Manager if i opened it "as administrator". Other VM's were in C:/Users/[user name]/VirtualBox VMs, they were owned by my user account and could only be seen if I opened the apps normally.

I was opening my Cygwin normally and therefore not being able to properly bring the VM back up (Still a little confused why reseting the ID each time seemed to work).

My solution: with help from this answer by thomthom

Within Oracles VirtualBox Mangager I changed the Default Machine Folder (File->Preferences->General) to C:/Users/[user name]/VirtualBox VMs. I then cloned each of the VM's so they ended up in the new directory. I then totally removed the old VM's (right click -> Remove) that were sitting in the cygwin folder. I then closed Cygwin and VirtualBox Manager and reopened as a normal users (VirtualBox Manager was not showing anything!)

Finally I went in the the new directory and double clicked each VM so it was added back into VirtualBox manager, then, fom the command line I ran VBoxManage list vms to get the new ID of the clones, copied that ID into the id file within my project (it will be something like PROJECT\.vagrant\machines\default\virtualbox\id

Now I can run vagrants "vagrant up" command with cygwin as a normal user and everything works great.

The lesson: Be very aware of what user you run the initial VM creations as, also be very aware of where VirtualBox manager is storing your VMs.