Hello and welcome to Apple Support Communities, SlightlyAnnoyed.
If I’m understanding your post right, you were unable to create a new playlist in iTunes using Autofill and your non-purchased songs in iTunes had exclamation marks and have also disappeared from your iPhone altogether. My personal iTunes library is filled with lots of music that was not actually purchased from iTunes and I would hate for them to disappear on me so I can certainly understand why this would cause you concern.
When songs show exclamation marks in iTunes, it means that iTunes isn't able to locate those music files on your computer. More than likely, when you connected your iPhone to iTunes it initiated a sync and since those music files could not be found when it synced, it removed them from the phone.
To answer your first question, yes, it may be possible to get your music back. However, getting that music back is really dependent on where that music is located. If your non-purchased music is being stored on an external hard drive, you would need to have that hard drive plugged into the computer in order for that music to work with iTunes. For some more information on how and where iTunes stores music, take a look at this support article:
Locate and organize your iTunes media files
If you're unsure where your non-purchased music is actually being stored, it would be best to follow the steps within that article for finding out the location first:
Locate the file for an item you see in iTunes
If you're not sure where iTunes stores your content, open the Get Info window:
- Select a file in iTunes.
- Mac: From the menu bar at the top of your computer screen, choose File > Get Info.
Windows: Hold down the Control and B keys on your keyboard to open the iTunes menu bar, then choose File > Get Info. Learn more about menus in iTunes for Windows. - Click the File tab.
- At the bottom of the tab, look to the right of "location" for the address or path where your file is located.

Some of your files might be stored in iCloud. For these files, Get Info shows iCloud instead of a path to a location on your computer.

Once you have located your music, if you would like to do so, you can add those songs to your iTunes Media folder. If you're using a Mac, you can locate the iTunes Media folder by selecting Go > Home > Music > iTunes from the Apple menu bar. If you're using a Windows computer, open
.
For your second question, yes, Autofill is still a function that works in the newest version of iTunes. Take a look at the following article for more information on Autofill, specifically the section that starts with "Fill your device with a random selection of songs using Autofill":
iTunes 12 for Mac: Sync iPod, iPhone, or iPad
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