running off an external startup disk

My internal drive is failing and i can’t afford to replace it for a while, so as of now it is wiped and I have Yosemite installed on a 64 GB mini flash drive, and am using that as my main startup disk. (I also have a 1TB external desktop hard disk with Yosemite installed, but am mainly run off the 64GB for portability issues)

I installed scrivener to the 64gb drive, in the Applications folder as usual, but when it starts up it says it is not installed correctly because it is not in the applications folder (even though it is). I checked the box to ignore this (after realizing that having it “fix” itself just deleted the program entirely), but it continues to come up every time I launch, and each time i have to put my license number in again.

Any idea what is going on/suggestions for how to get this to work? As i said, it will be quite some time until i can have a new internal drive installed, and i need to retain portability while still having full access to scrivener (I am disabled and as such cannot spend much time sitting at my desk, though i haven’t tried scrivener on the 1tb drive so i don’t know if it even works on there or not. regardless, i have to be able to work from my bed, couch, hospital, etc.)

I am having a similar problem with scapple, but scrivener is the more important one, so i’m posting about this issue here.

I’m not familiar with how well OS X in general runs on a flash-based thumb drive, I’ve heard of it being done, but I know nothing of its reliability. What it sounds like to me is that certain conditions are not being written to the disk. The flag that sets whether to ignore the message about the Applications folder is a preference, that get stored in a text file when you click it. And of course the registration info needs to be written to the disk as well. If nothing is being saved to the disk, anywhere, then neither of these functions would work. Can you make other changes, like setting a single preference (maybe toggle Show internal error alerts in the General preference pane), reboot or whatever it takes, and load the software up again. Is the checkbox the way you left it?