I’m also having a missing samples problem. My path was Cubase 6 → Cubase 7 → Halion Sonic Trial 1.5 → Absolute VSTi Instrument Collection → Cubase 7.5 → Halion 5 Upgrade Offer. My system initially reports 40 missing files and displays a Halion 3 instrument for which many of the samples don’t exist. HS Factory also has the missing Macro Page problem. I was able to get the number of missing files down to 10 by searching my entire C: drive; however, even the instruments that now will load show “No Macro page available” in the Edit → Macro tab. I suspect Steinberg failed to consider all the possible valid upgrade scenarios that qualify for their offer.
The simple fix would be to offer those of us having problems a full installer download instead of the upgrade installer download.