Hi,
I've investigated the issue on someone else's website and it seems to happen when the geolocation plugin is used with the option "after initialisation" activated in its settings. This results in HikaShop being loaded really early during the processing of the page, and HikaShop requests at some point the current template from Joomla, but Joomla hasn't had the time to load the correct template based on the Itemid as it didn't parse yet the SEFed URL of the current page and thus it defaults on the default template.
This is fine, but then, this causes Joomla to not recalculate the current template when Joomla has to call the template to display the page.
What's different between the 4.6.2 and previous versions is that in the 4.6.2 we fixed the override of class and controllers which didn't work properly before. And this leads to the template being asked quite early in the process of the page in such a configuration.
So deactivate that setting of the geolocation plugin and it should work fine, supposing that we're talking about the same issue.