I don't know if you use shared expenses or the EPT for your shared custody arrangement, but if she has proven not to pay her end of the direct expenses, that could put you in charge of them and give you a discount on child support. There are now a number of factors the courts must consider in which parent is in charge of DE, and that is one of them.
If you are entitled to claim the kids for 2016, then what I've been told is to simply file it and let the IRS deal with it. She will need to then file an amended return and pay her penalties.
If her change in income would have changed child support by more than 10%, she had a requirement to tell you - its in the guidelines (duty to notify). Use the tools at
[size=78%]https://efamilytools.com[/size] to determine if that's the case. If so, they should make any reduction in support effective back to the day her income increased. This will be a credit in your favor.
Your DRA will be very limited. Remember that if you "ballpark" your numbers, that's perfectly acceptable as long as you put an "*" next to them. Personally I used to put that next to every single number to keep myself in the clear and avoid having to calculate things to the penny.