Unchecked songs automatically removed from iTunes playlists after syncing

Hello, ever since I updated to the new iTunes (with Apple Music and stuff), I've noticed a very annoying pattern. I have unchecked songs in my iTunes playlists and each time I sync my phone, these songs automatically disappear from said playlists. The playlists now only contain songs that are checked (thus they look exactly as they are on my phone Music app.)

I find this a very very annoying and inconvenient matter, as I personally find the Check/Uncheck feature helpful.

I have 2 iPhones, one iPhone 4s 16GB I use regularly for communicating and one iPhone 6+ 64GB which I mostly use for entertainment purposes.

Since I listen to a lot of music (almost 10GB worth of music data), and as my regular phone, the 16GB 4s doesn't really have a lot of free space to spare, with all of my photos and documents and important apps,.. I check the songs that I listen to a lot recently and only sync checked songs to this phone.

But since my iPhone 6+ has a lot of free space and I mostly use it for entertainment anyway, I sync the entire music library to it. Checked and Unchecked songs alike. Since I occasionally listen to old songs too. Plus I can check/uncheck songs to keep the Music app on my iPhone 4s in order.

But the annoying remove the unchecked songs from playlists persists and each time I have to create, order the playlists again if I want the unchecked songs to appear on the playlists on my iPhone 6+, which is tiring and very inconvenient.

Has anyone encountered a similar problem? If you have any solutions please share, thank you.