You're conflating two things:
(1) situations where <spell> helps you, and
(2) situation where <spell> hurts you.
In the Clone scenario, you don't need Leomund's Secret Chest at all for a spellbook--you just keep your spellbook wherever you keep your clone, probably a Demiplane. Drawmij's Instant Summons can help retrieve your valuables (Staff of the Magi, Robe of the Archmagi, Ring of Free Action, whatever) that you lost when your last body died. Leomund's Tiny Chest can't retrieve those valuables. Score one for #1, "situations where Drawmij's Instant Summons helps you."
In the "all my stuff got stolen or destroyed but I'm still alive" scenario, which is the opposite of the Clone scenario, neither Drawmij's Instant Summons nor Leomund's Secret Chest will help you, because you don't have the tiny replica chest or sapphires. But in this situation, as long as the original stuff is not in a Secret Chest, you still have the ability to access the original stuff in its actual location, e.g. by Teleporting home after the adventure. You haven't permanently lost anything, you've just been inconvenienced. But if that stuff was in a Secret Chest, I'm sorry dude, it's gone. Score one for #2, "situations where Leomund's Secret Chest hurts you."
Hence why I wouldn't put anything truly important in a Secret Chest. You can if you want to--it's no skin off my nose.