I seem to constantly run into this problem where I will go back to work on a project that I haven't updated in a while. I will try to run the project and end up hitting bad fetches, and when I go to inspect I see that there are variables that are no longer present in the project.

For instance I have a collect node named CollectIvrToken. We read from this variable after it is collected and I can still see that variable and field is selected in a form node, however there is a warning telling me that the variable CollectIvrToken does not existing in the project, and sure enough it is not listed in the project variables.

How can I remedy these types of situations?

That's odd. I have never seen this problem. Try to redo the node?

Yes deleting and re-adding the component does fix the issue, however this leads to other problems such as having to go back to each place you had referenced this variable and ensuring they are all set correctly. Also any Node references are broken and have to be repointed. I was hoping for a more elegant solution. Is there a backing source file where these variables are stored and configured? Wondering if it has something to do with source control perhaps, maybe a file is becoming corrupted or changed on moving between branches or something.

I don't think source control would have corrupted the file. I am really baffled how the variable got lost. When the variable is gone and you save any change in the flow editor, you would have error marker showing up. That's how you go about fixing the flow. Unfortunately, there isn't anything easier than this.