Following William's lead, I did a little more digging.
In Mojave, these items are in the standard user account Preferences folder at /Users/<login name>/Library/Preferences/.
com.apple.Safari.plist
com.apple.Safari.SafeBrowsing.plist
com.apple.Safari.SandboxBroker.plist
com.apple.SafariBookmarksSyncAgent.plist
com.apple.SafariCloudHistoryPushAgent.plist
The same ones Marek noted. However, I found the same named com.apple.Safari.plist file in the location William showed. That one has today's date. The one in the standard Preferences folder was last updated June 27th.
Does that mean the .plist in the old location is now orphaned and no longer used? Or does the OS look at both? The former would seem more likely.
It would also be interesting to know what version of Safari the OP is using. That is, did the new .plist location begin with Safari 13.0, and removing it from the old location worked because the OP is still running 12.xx ?