At the geometry level, FBX represents meshes, hierarchy, rigs, animation, cameras and lights. STL represents a triangle surface with no scene hierarchy or semantic parts. A flattened surface can be dependable when the receiver only needs final triangles, but it is a destructive handoff when someone still needs editable solids, object hierarchy, animation, vertex attributes or manufacturing metadata. Once those semantics are discarded, converting the file back does not reconstruct the original design intent.
A safer production workflow keeps the richest editable source as the master and creates a separate delivery copy for a named destination. After export, inspect units, bounding-box dimensions, up axis, normals, watertightness, object count and material references in the receiving application. The main FBX caution is that it the format is complex, proprietary and prone to importer-specific differences. The main STL caution is that it drops units, materials, object structure and most manufacturing intent. These are workflow constraints, not minor technical trivia.
The practical verdict is to choose FBX when the job centers on animation and game-production exchange across established desktop tools, and choose STL when it centers on maximum compatibility with slicers, mesh repair tools and fabrication workflows. For 3D printing, the slicer's actual import is the final authority. Confirm millimeter dimensions, orientation and mesh integrity before generating toolpaths, even when the preview initially looks correct.