Don't use the backup utility.
Use the data transfer utility. It will copy over all copy-protected content from one PS3 to the other. Both need to be turned on and connected via Ethernet. Also, the PS3 receiving the data will have it's HDD formatted, so be aware of that.
With the new PSN access method, you should be able to run this utility and then login to PSN to activate all your DLC. Your saves should be fine.
60GB (120GB WD Scorpio Drive) PS3 (CECHA01, NTSC), 3.7OFW
60GB (640GB Samsung Drive) PS3 (CECHC04, PAL), Kmeaw 3.55, Repaired (Dead Laser)
PSP-1003 FAT, CFW5.00 M33-6 & Prometheus v2
X-Box 360 Xenon (JTAG'ed, 500GB HDD)