Is there hesitation or it just feels like it is lacking in power. That is actually expected when changing altitude. I kinda doubt it has to do with the flywheel. Usually that effects missfire counts and I don't believe those tables are available in RomRaider that I can find.
Some tables you can look at to improve your power at different elevations are Target Boost, Target Boost Compensation Multiplier and offset, Waste Gate Duty, Initial Waste Gate Duty compensation (ATM Pressure), Engine Load Compensation (MP), Timing compensation (MRP). All of these are closely related to altitude and you may or may not have to touch them.
Essentially you will need to tune specifically for the elevation you are at because the stock values in these tables are either geared toward emissions and safety or are not very well defined from the factory. You should also have a clear understanding of what your turbo likes to see so you need to become very familiar with the compressor map to determine the most ideal target boost for the elevation you are at. It may be quite a bit lower than you would think.
The good news is you don't have to do much fuel tuning provided you are properly tuned to begin with. If yours is a MAF based tune then the altitude is inherently compensated for automatically. :tup: