I think I'm making a little progress.
I exported the hikashop containing urls from JoomSEF, did a search and replace for 'hikashop and replaced all instances with 'store and imported back in.
Then inactivated all those hikashop containing URL's in JoomSEF and added an .htaccess
RewriteRule ^hikashop/(.*)$ /store/$1 [R=301,NC,L]
so I don't think I'll lose any incoming inquiries now but it's still not acting right. Some categories are now not displaying their products.
JoomSEF appears to be the problem but still - is there an easier way to deal with all this by bulk re-creation??