Is there a recommended level of skelebration for different modeling conditions?
This is largely up to your engineering judgment. However, different levels of skeletonization are appropriate depending on the intended use of the model. For an energy cost analysis, a higher degree of skeletonization is preferable and for fire flow and water quality analysis, minimal skeletonization is necessary. This means that multiple models are required for different applications.
For this reason, it is highly recommended that you run Skelebrator on a copy of the model. In addition to different levels of skelebration needed for different modeling cases, once some of the model has be skeletonized, you will not be able to revert back original dataset.
Additional information on using Skelebrator can be found in the Help documentation
Using Skelebrator to reduce the number of pipes in a model
How do you use Skelebrator on only a certain selection set of elements?