No big worries. It's more of an orginizational pain in the @$$ than anything else. All the individual object names are lost when you combine an object. When they're seperated out they just get generic numeric names. And you have to eyeball identify pieces and type in the names. If you've got a lot of objects that you combined the re-organization can take hours.
While I have sometimes run into gemetry artifacts with it (reversed normals, non existent geometry, faces with just wireframes and no actual surface) I haven't been able to narrow down the particular cause of said artifacts. These occured when getting a file from a 3rd party that came from another program as an obj or a dxf. These probably came from a CAD program of some sort, and were easily fixed by either asking for the file again, in a different format, exporting the corrupted data as a different format and reimporting, or just fixing the problem by hand.
But all of these problems are instantly obvious upon importing. If your geometry looks good it probably is.
Hope this helps.
-James