Yeah, I can replicate it but I'm afraid that I can't be much help. I have been suffering with the poor design of Halion's patch organization practically since I started using it a couple of years ago. My problems come from three sources:
1. Some of these patches came installed with older versions of some form of Halion, perhaps as a demo when I installed an early version of Cubase, like Cubase 5. Since then I have upgraded, via online download to Cubase 6 and then Cubase 7. When my hard drive died earlier this year, I reinstalled Cubase 7 (and Halion of course) and noticed that there were missing samples in Halion. Then I realized that some of those samples came with the earlier install of Cubase 5. So I had to find those discs and try to load those samples without having to install the earlier version of Cubase. PITA
2. The whole reason that I purchased Halion in the first place was that it would import my multitude of Gigastudio (a program that no longer exists) samples. But the organization of those samples is poor as well. The problem is that I use Cubase and Halion on two different machines, a desktop in my studio and a laptop for remote recording and composing. I have imported the Giga samples to an external drive to be able to use them on both machines. BUT. Halion imports the AUDIO to the external drive but not the patch file that tells it what to do with the audio. That gets stored on the machine. Which means that when you go to load a Cubase project on the machine that you DIDN'T import the Giga sample into, Halion won't be able to find it because the patch file is stored on the other machine (in some endless mysterious series of system folders that even the Steinberg techs have a hard time identifying).
3. Having two machines has compounded the problem in another way too. I have tried to keep both machines current and duplicated so the same identical software is on both to make loading a project in either machine go smoothly. All other software but Halion works in this way. Because of the issue in #1 above, there are some Factory Content samples that seem to be installed on one machine but not the other. So even when I load a Cubase project with Halion Factory samples in it, some of the Factory Patches turn up missing and no amount of "rescanning" seems to help.
There IS a "rescan disc" button on the "Load > Media Bay" page in the bar in the middle on the right (hover over it to see it say "rescan disc") but I have had limited success with it.
I have worked with a tech via email a couple of times on this issue and haven't really had any success.
As I said, I really haven't experienced this kind of software data problems with any other aspects of my digital audio software. It is frustrating.
I wish you luck. I'd love it if Steinberg could redesign this aspect of Halion in some way.
Desktop: Cubase 7.5.30 Wavelab 8.5.10, Halion 5.0.1, Presonus StudioLive 24.4.2AI, CPU Intel Core i7 3.4gHz, Motherboard Asus P8z77-v LX, 16gb RAM, Video Card MSI R5450 (no fan), PSU Zalman ZM600 HP, Zalman Reserator 1 liquid cooled system, Windows 7 x64 Home Premium, Pro Tools 9.0.6, Waves Mercury Native 9r20
Laptop: MacBook Pro (15 in), 2.4 gHz Intel Core i7, 8 gb RAM, OSX Mavericks 10.9, Focusrite Saffire Pro 14 (Driver v 3.2), Presonus StudioLive 24.4.2AI, Philips DVD+-RW SDVD 8820 SATA drive, Wavelab 8.5.10, Cubase 7.5.30, Halion 5.0.1, Pro Tools 9.0.6, Waves Mercury Native 9r20