Not knowing the detail of the complex algorithms I return to the reply of Guy which has an important part about the kind of data. Having seen this throw issues on imported data for missing key information it will not recreate the missing fields. Also it only checks the elements it is programmed to check, it does not check everything. I think for the whole life of AX2009 it was based on the AX4 table structure :-) So it tells you issues of the elements it is designed to check and will only fix these if it is possible to fix them.
Ultimately run it, some are warnings you can do nothing about, but analyse it. I would not run the fix unless it was related to specific data I could not correct from the UI and I thought perhaps the fix would fix it, but I would not hold hope that it necessarily would!
Get a developer to look at the code and extrapolate the complex algorithms.