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On the umpteenth time it finally restarted but it's only temporary so I'll start doing this stuff tonight.

There is no data on it which originated on it - or very little. Proper backups are impossible as the Mac won't talk to it except via Android File Transfer.

What I will do is a series of screen shots to remind me what apps I find most useful though presumably whatever corruption has happened may be down to them anyway.

If it is factory reset, what will the Play Store do once it finds a "naked" phone? Presumably the fact that it knows some apps are installed or even paid for is a factor of the phone and not the Store?
 
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The Play Store keeps your information in a pristine state. I still have programs listed I downloaded when I got the G1 from t-mobile that was back in 2008. I never paid for anything back then. I think it's linked to the Gmail account you use when you go through the setup process again. Google is anal about that type of thing.
 
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So there are only things installed 'off store' to worry about.

A factory reset as described will wipe your phone except for your media. When you restart and log into your Google account it will start downloading all the apps you have ever gotten from there, unless you disable sync. It is not an option for Google play store, but uncheking everything under settings>general>accounts>Google will stop it. You will (or should do) restore all your app data if sync is set to do so, not wise if you think your issues are to do with clashing app data. "Off store" apps will need to be reinstalled manually (side loading), stick the .apk files for them in a folder called apps on your external SD card and reinstall them from there. My guess is it is one of these that is causing you problems though.
 
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On the umpteenth time it finally restarted but it's only temporary so I'll start doing this stuff tonight.

There is no data on it which originated on it - or very little. Proper backups are impossible as the Mac won't talk to it except via Android File Transfer.

What I will do is a series of screen shots to remind me what apps I find most useful though presumably whatever corruption has happened may be down to them anyway.

If it is factory reset, what will the Play Store do once it finds a "naked" phone? Presumably the fact that it knows some apps are installed or even paid for is a factor of the phone and not the Store?

You can backup the note 3 with the app "my backup pro" & OTG cable to a usb stick, and/or "my backup pro" to the sd card.
I backup my Note 3 with both this options, and don't use my mac for this.

See link for some more info about my backup pro
MyBackup Pro for Android takes care of all your backup needs [Hands on Video] | TalkAndroid.com

If you go for the backup via a usb stick, you first should change the settings in my backup pro, the default setting is via sd card.
 
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You can backup the note 3 with the app "my backup pro" & OTG cable to a usb stick, and/or "my backup pro" to the sd card.
I backup my Note 3 with both this options, and don't use my mac for this.

See link for some more info about my backup pro
MyBackup Pro for Android takes care of all your backup needs [Hands on Video] | TalkAndroid.com

If you go for the backup via a usb stick, you first should change the settings in my backup pro, the default setting is via sd card.

Another vote for My Backup Pro. Excellent piece of software.
 
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Have you tried booting into Safe Mode?

With the device powered off, press and hold the Volume Down + Power buttons together. When the Note start up screen shows, release only the Power button. Keep holding down the Volume Down button until it is booted. You should see Safe Mode on the bottom left corner of the screen.

If you suspect an app that is causing the issue, you can uninstall it in Safe Mode. You cannot use any apps except the default ones that came preloaded in the Note I believe. This might help troubleshoot the problem further.

To exit Safe Mode, simply restart the device as usual.
 
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All my non-simcard phone directory is completely gone: Names, numbers (some had 8 per entry), email addresses and all associated pictures. Something else to ensure I have backups of in future.

Check on your linked Gmail account (the one you needed to set up the Google Play Store account)
Chances are that your contacts were backed up to your Google account at some point in time during initial phone set up, even if you told the phone to not back up contacts at a later time.

There is also a way to view ALL the applications that have been downloaded by your Google Account. The ones you are "missing" might have a log there, but were not part of your recent restore. You mentioned you had some side-loaded applications, those will not be restored by the Play Store, and may be part of the contingent of applications you are missing.
 
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