Even when using proper representation, the TP should still have basic knowledge to spot something this and/or hiring out for at least a cursory review. I mean really, a S Corp which does not zero out each year? I am not discounting the allowed practice of things like holding checks, for even months, to defer income, but to what sounds like cash checks, but claim then as undeposited/unrealized? Maybe the bookkeeper is also a sovereign citizen :).
As I sit in a home where I either DIY or pay licensed insured for repairs/maintenance, and next door, they are finishing up unpermitted window and roof replacement with unlicensed employees on a slow work day (and run an unlicensed, unpermitted, and not allowed cash business from their home).