This sounds like a case for Sherlock Holmes.
If you checked the ground to make sure they were not knocked off by wind, rainfall or hail, not impossible given the absolutely torrential weather events seen over the past few weeks, then logically all that remains is pests.
The most likely candidates being two legged. Pigeons can perch on nets and cause a surprising amount of damage even when crops are covered. And if you are not careful can sometimes get underneath if the nets are loose. But destructive as they are, the ability to remove nets, pick fruit and then put the net back may be beyond them.
I'd suspect other two legged pests, which is also very very sad.