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If you can tell us what Adobe application you're using and which version, we can send your question to the proper forum. You haven't provided that information.
After Effects CC (12.2)
There is nothing inherent in a pre-comp that causes loss of quality. If you have vector art or are working with 3D layers you can collapse transformations to help with scale issues. Usually when someone has this problem they are new to AE and are not using the proper workflow or techniques. Without screenshots that show the entire UI with the modified properties of the layers giving you problems revealed (press the u key twice) and the same thing for your pre-comp (nested comp) it's impossible to tell you exactly what's going on and how to fix the problem.
If you have no idea what collapse transformations does then study up using the Search Help field in AE. If you've tried everything else then we need screenshots and details.
Are you still facing this problem? If not, let us know how you solved it. If so, please let us know so we can assist you further.