Hello, Cuslichavy.
Thank you for your interest in our product and welcome to our forum. And don't worry about questions, we're here to answer them

1. ReHIPS doesn't disable any other program security features and doesn't try to bypass or circumvent any of them, so no it shouldn't compromise any other program security including sandboxing.
2. Do you mean you can do it technically? Or should you do it? Technically no, if a program is isolated, it can't start other programs without isolation. Should you do it? It depends. If it's something trustworthy, why not. But I prefer to treat isolated programs as potentially compromised, so nothing goes from isolation out.
3. Can you give an example of different folders after update that causes a headache? Something like different version numbers in folder name? You can use wildcards to cover folders like this.
4. C:\ReHIPS subfolders are to exhange data with isolated programs. Like you want to edit a .doc-file, you put it there and edit it with isolated Word. Here is a blogpost about it
https://forum.rehips.com/index.php?topic=9487.0 So putting a program in that folder isn't supposed to start it isolated. To create other folders simply create a new folder and give isolated environment permissions to it.
5. Wildcards are covered in this blogpost
https://forum.rehips.com/index.php?topic=9647.0 Most likely there are multiple level of folders and you wildcarded only one level. Either wildcard all of them or wait for the next release where ** wildcard should be supported.
6. ReHIPS suspends a starting program at a very early state where it hasn't begun executing, so most likely ReHIPS did its thing OK and these few search results you observed were taken from elsewhere, maybe from cache, maybe some internal search is also started in parallel or something like this.