Hi,
When the store is put offline, it doesn't generate a 404 error. It just put a message on all the pages and skip their display and the potential processings.
So when you put it back online, it shouldn't generate a 404 error either.
So I'm thinking that the issue you have is not linked to that setting at all.
To me, it looks like a SEF problem.
For example, if you reset the cache of sh404SEF (supposing that you're using that extension) and that you have canonical URLs in your products and that you configured the system to force canonical URLs (with the setting in the Hikashop configuration), you would end up with URLs to your products/categories which have not been stored in sh404SEF URL cache.
In such case, it would result in the exact thing that you currently have: the links are correct on the listings but when you click on it they give back a 404 error.
In that case, there would be several things you could do:
- restore the cache of sh404sef from a backup
- clear your products/categories canonical URLs (you'll have to reenter/regenerate them afterwards)
- turn off the "force canonical URLs on listings" setting so that the URLs are regenerated dynamically and sh404SEF can reindex them.
Now, I don't know whether or not you're using that extension, if you have canonical URLs for your products/categories nor how the settings in the "SEF" section of the HikaShop configuration are setup, so I'm just speculating here.