Weird NSUserDefaults/CFPreferences behavior. See https://twitter.com/tempelorg/status/1117388426221846529

console output

i: 165
r0: 165
r1: (null)
r2: 165
r3: (null)
r4: 175

good and bad ones

// path contains the full path to the plist file, whereas domain contains just the suite name.

// good
CFPreferencesCopyValue((CFStringRef)key, (CFStringRef)path, kCFPreferencesCurrentUser, kCFPreferencesCurrentHost);
CFPreferencesCopyValue((CFStringRef)key, (CFStringRef)path, kCFPreferencesAnyUser, kCFPreferencesCurrentHost);
CFPreferencesCopyValue((CFStringRef)key, (CFStringRef)path, kCFPreferencesCurrentUser, kCFPreferencesAnyHost);
CFPreferencesCopyValue((CFStringRef)key, (CFStringRef)path, kCFPreferencesAnyUser, kCFPreferencesAnyHost);
CFPreferencesCopyValue((CFStringRef)key, (CFStringRef)domain, kCFPreferencesCurrentUser, kCFPreferencesAnyHost);

// bad:
[NSUserDefaults.standardUserDefaults integerForKey:key];	// stuck value
CFPreferencesCopyAppValue((CFStringRef)key, (CFStringRef)path);	// stuck value
CFPreferencesCopyAppValue((CFStringRef)key, (CFStringRef)domain);	// stuck value
CFPreferencesCopyValue((CFStringRef)key, (CFStringRef)domain, kCFPreferencesCurrentUser, kCFPreferencesCurrentHost);	// stuck value
CFPreferencesCopyValue((CFStringRef)key, (CFStringRef)domain, kCFPreferencesAnyUser, kCFPreferencesAnyHost);	// null
CFPreferencesCopyValue((CFStringRef)key, (CFStringRef)domain, kCFPreferencesAnyUser, kCFPreferencesCurrentHost);	// null

log output

// log for the affected app after using:
//  sudo log config --subsystem=com.apple.{defaults,cfprefsd} --mode "level:debug, persist:debug"
// and to turn that logging off again:
//  sudo log config --subsystem=com.apple.{defaults,cfprefsd} --reset

42.491434	cfprefsd	Process 1565 sent a request related to { org.tempel.faf2, user: kCFPreferencesAnyUser, kCFPreferencesCurrentHost, no container, managed: 0 }
42.491514	cfprefsd	Process 1565 sent a request related to { org.tempel.faf2, user: tt, kCFPreferencesCurrentHost, no container, managed: 1 }
42.491440	cfprefsd	Process 1565 sent a request related to { org.tempel.faf2, user: kCFPreferencesAnyUser, kCFPreferencesCurrentHost, no container, managed: 1 }
42.491516	cfprefsd	Process 1565 sent a request related to { kCFPreferencesAnyApplication, user: tt, kCFPreferencesCurrentHost, no container, managed: 1 }
42.491445	cfprefsd	Data for { kCFPreferencesAnyApplication, kCFPreferencesAnyUser } was purged due to memory pressure
42.491518	cfprefsd	Process 1565 sent a request related to { org.tempel.faf2, user: tt, kCFPreferencesAnyHost, no container, managed: 0 }
42.491487	cfprefsd	Couldn't open <private> due to No such file or directory
42.491535	cfprefsd	Process 1565 sent a request related to { org.tempel.faf2, user: tt, kCFPreferencesCurrentHost, no container, managed: 0 }
42.491493	cfprefsd	Process 1565 sent a request related to { kCFPreferencesAnyApplication, user: kCFPreferencesAnyUser, kCFPreferencesCurrentHost, no container, managed: 0 }
42.491551	cfprefsd	Data for { kCFPreferencesAnyApplication, <private> } was purged due to memory pressure
42.491525	cfprefsd	no cache for { kCFPreferencesAnyApplication, kCFPreferencesAnyUser, kCFPreferencesCurrentHost, no container, managed: 0 }, loading from /Library/Preferences/.GlobalPreferences.plist
42.491551	cfprefsd	Data for { kCFPreferencesAnyApplication, <private> } was purged due to memory pressure
42.491577	cfprefsd	Process 1565 read data for { kCFPreferencesAnyApplication, kCFPreferencesAnyUser, kCFPreferencesCurrentHost, no container, managed: 0 }, backed by /Library/Preferences/.GlobalPreferences.plist
42.491554	cfprefsd	Process 1565 read data for { org.tempel.faf2, tt, kCFPreferencesAnyHost, no container, managed: 0 }, backed by /Users/tt/Library/Preferences/org.tempel.faf2.plist
42.491572	cfprefsd	Process 1565 read data for { org.tempel.faf2, tt, kCFPreferencesCurrentHost, no container, managed: 0 }, backed by /Users/tt/Library/Preferences/ByHost/org.tempel.faf2.21A029CC-8327-558F-BFB3-EB038C8CE205.plist
42.491581	cfprefsd	Process 1565 sent a request related to { kCFPreferencesAnyApplication, user: tt, kCFPreferencesCurrentHost, no container, managed: 0 }
42.491586	cfprefsd	Process 1565 sent a request related to { kCFPreferencesAnyApplication, user: tt, kCFPreferencesAnyHost, no container, managed: 0 }
42.491661	cfprefsd	no cache for { kCFPreferencesAnyApplication, tt, kCFPreferencesCurrentHost, no container, managed: 0 }, loading from /Users/tt/Library/Preferences/ByHost/.GlobalPreferences.21A029CC-8327-558F-BFB3-EB038C8CE205.plist
42.491728	cfprefsd	no cache for { kCFPreferencesAnyApplication, tt, kCFPreferencesAnyHost, no container, managed: 0 }, loading from /Users/tt/Library/Preferences/.GlobalPreferences.plist
42.491820	cfprefsd	Process 1565 read data for { kCFPreferencesAnyApplication, tt, kCFPreferencesCurrentHost, no container, managed: 0 }, backed by /Users/tt/Library/Preferences/ByHost/.GlobalPreferences.21A029CC-8327-558F-BFB3-EB038C8CE205.plist
42.491873	cfprefsd	Process 1565 read data for { kCFPreferencesAnyApplication, tt, kCFPreferencesAnyHost, no container, managed: 0 }, backed by /Users/tt/Library/Preferences/.GlobalPreferences.plist 

prefscheck.m

- (void)applicationDidFinishLaunching:(NSNotification *)aNotification {
	NSUserDefaults *prefs = [NSUserDefaults standardUserDefaults];
	NSInteger i = [prefs integerForKey:@"SearchCount"];
	[prefs setInteger:i+10 forKey:@"SearchCount"];
	NSInteger r0 = [prefs integerForKey:@"SearchCount"];
	CFPropertyListRef r1 = CFPreferencesCopyAppValue(CFSTR("SearchCount"), CFSTR("/Users/tt/Library/Preferences/org.tempel.faf2"));
	CFPropertyListRef r2 = CFPreferencesCopyAppValue(CFSTR("SearchCount"), CFSTR("org.tempel.faf2")); // same as kCFPreferencesCurrentApplication
	CFPropertyListRef r3 = CFPreferencesCopyValue(CFSTR("SearchCount"), CFSTR("/Users/tt/Library/Preferences/org.tempel.faf2"), kCFPreferencesCurrentUser, kCFPreferencesAnyHost);
	system("defaults read org.tempel.faf2 SearchCount >/tmp/r4");
	NSString *r4 = [NSString stringWithContentsOfFile:@"/tmp/r4" encoding:NSUTF8StringEncoding error:nil];
	NSLog(@"\n%ld\n%ld\n%@\n%@\n%@\n%@", i, r0, r1, r2, r3, r4);
	exit(0);
}

For anyone finding this and looking for a solution: I eventually found a file inside /Users/tempi/Library/Preferences/ByHost that contained all the "stuck" preferences.

I identified this file by using FindAnyFile, looking for any files modified in the past 2 days, and with the File Content containing one of the stuck keys.