Creo is more than capable of managing very large number of references between models consisting of complex geometry. The high feature count or numerous references is not likely the source of your issue. Merge and solidify features failing is likely doe to the nature of how the model was originally constructed. I see this type of instability in models built using surfacing quite often, it is usually a result of how the features were defined when created. Does the generic model have geometry checks? Without models to query the determination of a cause of the issue is difficult.
When you query geometry checks, so you see this attached to any merge features in the model?
- Merge surfaces warning:Design intent is unclear. Use "Info"/"Geom Check" menu for details.
- Warning In Troubleshooter dialog box
- The boundary of the highlighted surfaces was extended. Unexpected results are possible.
- Recommended actions: Try to modify the feature so that extending is not necessary.