You ask 'What should I do? and I would say that you should... do nothing. Don't worry about it. There's nothing important about the number selected, and no harm in it having jumped to a larger value.

But that said, if you really want the numbering to reset, take a look at the File Numbering option in the menu (see page 191 of your manual). Change it to "Auto Reset", and the next time you format your card, it'll go back to zero. If you then want to continue from there without resetting again, simply put the T back to "Continuous".

I haven't tried it, but I expect that if, once you've reset and then changed back to continuous, if you copy one of your photos with a higher number back to the card and take a shot, it will continue from there.

But, going back to my first point, I think relying on the camera's naming just isn't best practice. You say ". I can't change the fact that Canon set none-unique (e.g. date based) or not-long (5-9 digits) numbers, so the only thing I can do is to have numbering progressing slowly." But actually, there is something you can do: rename the photos as you import them, with a scheme based on the date and time. There are many, many programs that do this. I use ExifTool as part of a script which copies images from my memory cards, but there are many others.

I recommend this because, as you note, 4 digits isn't really that many, and keeping the files with their original short names just seems like a problem waiting to happen someday in the future.