Keep an untouched copy of the input mesh and apply one cleanup step at a time. Inspect holes, normals, and thin features before simplifying, then compare the result with the original at a useful scale. Test the exported file in the destination application, since a clean-looking surface may still fail downstream geometric requirements.
This is best suited to users repairing and preparing scanned mesh geometry. Before committing a larger project, account for these trade-offs: destructive filters need careful review; not a full parametric CAD system.
