Try viewing ALL.
I find that Amazon removes books from Collections, but not the device.
Also only Download direct to PC and never Sync. I have quite different generations of Kindles and any Sync messes up Collections.
I've actually given up on collections on the Kindle except for titles I testing. My wife also has a Paperwhite 3 and has recently got a Kobo Libra because Collections and Series work properly from Calibre (though you have to connect twice) and the page turn buttons are handy when eating toast.
It's only the price of 10 to 15 non-discount books from a bookshop.
I'd be nearly certain it's just filter settings. Make sure you view all.
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