I refer you to the ATA100 data discussion in the military forum, as well as earlier editions of the MT milcom blog. To summarize, the top data comes from the FAA and is not necessarily the most accurate of data dumps; however, they do list several discrete and 'do not publish' freqs not found elsewhere.
Your best bet is probably to merge the 2; take the discrete and do not publish freqs (don't expect to hear a lot of traffic on them...) and use the bottom lists as your main source of information.
As mentioned in the discussion, there seems to be a number of shifts going on at the moment - partly because of the 380 Mhz TRS situation, other reasons are unknown right now. The ZDC and ZNY regions have had 5 or 6 new freqs, and more are expected; and it can be reasonably expected other regions will also be shifting. The only way to know exactly which new freq is being used by what sector is 2 words careful listening