PIM Sync and Address Book backup
Don't assume that Blackberry device address book is backed up to the server via wireless just because it is synchronized to a user's PAB. Some important fields are not synchronized in the default configuration. Use the PIM Sync field mapping. Note that at the user level you can also backup the device "Picture" field. Unfortunately in BES 4.1.6 you can't set this using the global PIM Sync Field Mapping.
Is wireless backup enough?
Not if your users take photos, or rely on old messages in their folders or inbox. There are several things that are not backed up wirelessly.
Good idea to remove and re-add BES User for troubleshooting?
Maybe not. Deleting the BES User from Blackberry Manager breaks the link between the device and the server. The state database which stores this information will become disassociated permanently from the users profile. If the user relies on old messages in inbox or folders they may be unhappy.
More than one Desktop contact list?
Newer devices like the Blackberry Bold (handheld code 4.5 or higher, I think) allow multiple contact lists. One contact list synchronized with corporate desktop, one for personal, one for sharing with your family using some new-fangled software. Nice idea, but not 100% yet. Unfortunately changes to PIM Sync settings (or cosmic rays, high tides) can create a second (or third, or fourth, ...) contact list called Desktop which populates from the server usually creating duplicates of every contact. The only way I've found to get rid of these extra contact lists is to wipe the handheld (2008Oct30). Perhaps RIM will provide a less disruptive method soon.