Painting makes the flocking tougher when done properly, but how they hold up depends on how well you care for your decoys. Flocked decoys aren't for everyone, if you like to texas rig your decoys and toss them into the back of your pick up, then flocked decoys probably aren't a good choice. Decoys are one of my most important tools in duck hunting and I'm not careless in how I use them. I hunt hard, but I don't throw my decoys around any more than I throw my shotgun around. All decoys, flocked or just painted, show wear over time, especially if they are abused. I use slot bags, but don't single bag the decoys unless they are going into the same slot with another decoy, keeping them from rubbing against each other is important. Using paint compatible with the glue is also important to adhesion and durability. There are many components to flocking durability and adhesion as well as paint adhesion, things that have to be addressed are chemical, mechanical, technical, thermal, viscid, encapsulation, fusion, coadunation, and UV degredation. Most commercial flocking jobs only address one or two of these issues, that's why they fail over time, but of course nothing is going to last forever, but you can make things last longer than factory flocking. We have a proprietary process that involves 29 steps, most companies use 3 steps. Paint adhesion has as much to do with technique as it does with paint type.
This is a photo of some of my decoys after a full season. The flecks of stuff on them is weed debris, two black ducks and a mallard hen.
The goldeneye drake decoy on the left is 6 years old. The green is still holding well after 6 seasons and it goes with us on every hunt. The white has been repainted once over the past 6 years.