I wouldn't worry about it too much..

Just did a quick search and found a comment by a guy in your position.

I have done this , I pushed off to Saudi for a couple of years to work.
I missed 2 Annual reports, When returning to the Philippines, It was no bother at NAIA, stamped through as usual , { As a 13a holder } & then when reporting to Immigration here in Bacolod, No drama's , just paid the missed annual report fee's { P260 } & all was right with the world again !... incredible !!!.
He said this in 2014 so rules might have changed..I have no clue. IMO you will pay any fines due (if any) when you report early next year...If the worst comes to the worst and your visa is now invalid,at least you are travelling with your Mrs so they will give you a BB stamp..(one year visa free stay)
Anyway..Let us know how you get on.