The limit is simply that the ID of a new question must not exceed 99. SoSci Survey will always use the next available ID, so if a section has only a single question, but that uses the ID 98, then only one more question is possible.
You can move questions between sections or reset the numbers (so they start from 1 in each section), as described above. This is possible in an existing survey project and in a copy of the project, alike. The only reason not to reset the ID numbers would be that you're already collecting data, or that extensive PHP code refers to the current IDs.
> If I create a new Survey project in order to redistribute the total number of IDs
If none of the above restiction appies, creating a new survey project seems not neccessary to me. If I got the situation wrong, please go more into details.