Don't know what you did with the code so can''t give you more than:
- There is onviewchange event used that is checking current zoom level and make some hotspots invisible.
So it might be that you have to remove this event before loading new pano not to be active on your new scene and not making your hotspots invisibe there too.
Easiest way is to make this event not global but local:
Change
<events onviewchange="checkfovchange();"/>
to
<events name="somename" onviewchange="checkfovchange();"/>
Without keep="true" it will be removed when loading new pano.
Reference for you:
http://krpano.com/docu/xml/#namedevents