How to prepare (compress/zip) a plugin to enable updating instead of adding new instance?

I created my own plugins and install/update them by uploading the zip file in the dashboard. That worked well, but suddenly¹ a new instance of the plugin gets added instead of updating the already installed one. Before WP would ask do you want to replace version X with version Y, but that dialog does not appear anymore.

I had this issue before, but back then I had the date and version in the name of the zip file. Ever since I always use the same name for the zip file (e.g. my-plugin.zip), it used to update the plugin.

Now WP creates new directories my-plugin-1, my-plugin-2, ... when updating.

Is there a best practice for creating the zip files?

What let's WP decide whether to install a new instance or update?

Update

It seems that it now works again as before, the zip files are recognizes as updates. I have no clue why it stop working nor why it started working again.

I would still be interested on how to best prepare (compress/zip) plugins to enable an update instead of adding a new instance.

Is it the name of the zip file? The name of the zipped folder? The name in the style.css manifest?

¹ I'm sure there is a good reason for it, but I don't know yet what changed that caused this