Modules dissappearing.

That's a problem of Itemid.
In joomla, each menu generated has an Itemid linked to it. When you assign a module to a menu, in fact, all the links with the parameter Itemid equal to the menu Itemid will display that module.

At first, we didn't had any Itemid in our links in HikaShop. Now HikaShop always adds the Itemid parameter the urls so that you keep your modules while navigating your store.
However, it depends on the options you set in your menus and modules.
For modules displaying a list of product and which are not synchronized with the option "content synchronization", the Itemid used will be the Itemid of the menu you can set in the options of the module.
For modules displaying a list of category, the itemid used will be the itemid of the menu you can set in the options of the module.

In all other cases, the links will keep the Itemid of the current page so you will keep the current modules.

So to conclude, it means that you should make sure that you are using at least the version 1.3.0 and that your modules have the option "menu" set to the appropriate value.

Did you set the module which disappear to appear only on certain pages on the joomla options of the module ? If yes, then, in the HikaShop options of the module where you click on the product, you need to set the menu option to one of the pages to which you limited the other module.
Otherwise, it could be that the module which disappear has the option "content synchronization" to on, so you should turn it off.

Yes, it's indeed not easy to setup. Unfortunately, that's how joomla works...
We want to provide in the future preconfigured modules and menus so that you don't have to configure all that by yourself which should already greatly simplify the process.

For the menus appearing although your removed them, I just checked on a test website and after removing the menu and then removing it from the bin menu, I couldn't see it anymore in that dropdown. The menus displayed in that dropdown come from the joomla menu table. IF they are displayed there, it means that there are still in the joomla menu table... There is nothing we can do about it :/

Normally, on the latest versions of HikaShop, we added some code to set the itemid in the URL for the checkout. Maybe you have edited that view ?

Could you check on the Display->Views menu for the cart file of the view product if you have a customization ?

If so, you can either delete the customization, but you will loose your changes, or try to modify the code:
We added the code :
global $Itemid;
$url_itemid='';
if(!empty($Itemid)){
$url_itemid='&Itemid='.$Itemid;
}
near the beginning of the file and then, we change the form action URL to add the .$url_itemid at the end:
echo hikashop::completeLink('product&task=updatecart'.$url_itemid,false,true);
and at the end of the checkout button URL:
hikashop::completeLink('checkout'.$url_itemid)