I could see a couple reasons for this.
1 could be that the particular app in question is just not compatible with IOS9 at the moment. Sometimes IOS updates break applications until the content creator can update the app to be compatible with the new IOS version.
Another reason could be due to a profile setting you may have. If you have Profiles pushed to the iPads, check your Age Limits, if age restrictions are set an app may be blocked (Browsers are listed as PG-13 and blocked after certain updates) causing their icons not to show up even though technically they are on the device.
The final reason (and more likely) I could see would be that if you did a restore (thru recovery, and not a update) it will wipe the device and you will lose both your apps and your codes. VPP codes can only be given and taken back by configurator. If you wiped the device thru recovery you have removed the configurators abililty to recover then codes and then reuse them. Thats why Apple always states to unsupervise a iPad before resetting so that you get your codes back (your remove the app manually thru configurator by unchecking the box for the app and then refreshing). If this is the case and you wiped the device before recovering the keys you have two options: Call Apple's VPP dept and see if they will be nice and give you new keys, or you can manually log in with the Apple ID associated with the app and redownload manually on all the iPads (since you paid for them, you are entitled to that many downloads).
