Differences between NetAffx Hg-U133 Plus 2.0 Annotation file versions
After checking the files myself, it does seem like gene identifiers indeed have been updated. Some that were missing have been added with identifiers and some have additional identifiers now.

Among some other things that were updated from 2007 include:


Genome version NCBI Version 36.1 => GRCh37
Alignments
Gene title
Gene symbol


Thought this would be a good reference for those who may be looking into older researches involving microarrays. I will be sure to check the files more carefully before posting questions like this one.