The question is too broad to be answered accurately however, the answer is definitely maybe!!
You fail to mention what ISO you will be booting from. Since we don't know, it means the answer is yes, it could have malicious code which destroys data, it could have legit reasons, such as storing information about the session or configuration changes. It could make useful changes to the registry to fix issues. So, as you can see it can make changes for good or bad.
The fact you're using it suggests it probably comes from a trustworthy source, making it more likely to not damage your files, but the answer is yes, booting from an ISO can affect files. Whether it will or not, we can't answer.