Creating, modifying, or removing hosting projects will not affect a questionnaire file in Lighthouse Studio. The only time where hosting can impact what is going on in Lighthouse Studio is when you download data from a hosting project to your local computer. Even then, that only changes the questionnaire's data, not the questionnaire's settings (questions, exercises, passwords, etc.). As long as there's no data on a hosting project that you need to keep around, you can safely delete the project.
That being said, I know many Lighthouse Studio users make copies of their questionnaire files and/or respondent data before making any significant changes. It shouldn't be necessary in your situation, but it's easy to do and can provide some peace of mind knowing you have backups of your work.