I recently updated my MAC MINI to El capitan, when it restarted my Harmony was still linked and worked great, however after a second restart, it did not, it showed that it was still registered with Remote buddy but not connected a restart of Harmony the MAC etc etc did not restore the link.

So then I removed the remote and then just wanted to reconnect it, thinking this would work....

However it did not, now on my Harmony it comes up with the PS3 instructions for pairing so is in pairing mode, Remote Buddy searches but then just keeps searching..... never finds anything.

I have tried deleting my Harmony profiles for the PS3 and setting up from scratch 
Removing Remote Buddy and reinstalling 
Resetting Harmony

However nothing works..... Any help would be really appreciated as I love the Remote Buddy system so much,now I have to use the Harmony and my Iphone app to get it to work.

Really appreciate the time. 

I can see two possible reasons for this:

A) your Bluetooth settings got corrupted. 
B) the Harmony Hub doesn't attempt pairing long enough.

Solution 1 for A: Resetting Bluetooth settings 
1) Delete the Bluetooth settings files by entering this into Terminal.app: 
sudo rm /Library/Preferences/com.apple.Bluetooth.*.plist 
sudo rm ~/Library/Preferences/ByHost/com.apple.Bluetooth.*.plist 
2) Reboot 
3) Retry pairing.

If pairing still does not work, Bluetooth may need a more thorough reset:

Solution 2 for A: Resetting Bluetooth settings and hardware 
1) Delete the Bluetooth settings files by entering this into Terminal.app: 
sudo rm /Library/Preferences/com.apple.Bluetooth.*.plist 
sudo rm ~/Library/Preferences/ByHost/com.apple.Bluetooth.*.plist

2) Hold down Shift+Alt while clicking on the Bluetooth icon in the menu bar. This gives you an entry called "Debug". Inside the "Debug" menu, choose "Remove all devices", then "Reset the Bluetooth module".

3) Reboot.

4) Retry pairing.

At this point, pairing should work. If it still does not, you may have stumbled over an issue I've run into myself recently, which brings me to…

Solution for B: 
With the latest version of the Harmony App for iOS, I noticed that the Harmony Hub only briefly attempts pairing when it brings up the screen and will attempt to only once – even if you go back and forth to/from the previous step.

The solution there is to open Setup Wizard in Remote Buddy and have it look for devices already before the Harmony App gets to the Pairing step.

Once that step has arrived and a few seconds have passed, the only way I found (during setting up a new PS3 Remote device) to get another chance for pairing was to delete the device and create it anew.

I hope this bug in the Harmony app/hub will be be addressed by Logitech with a future release.

If possible, please let me know if the above helped you resolve the issue.

Cheers, 
Felix 

Thanks for the response.

I tried as you mentioned to reset the software and hardware settings, this had no effect. Still the same "searching for remotes".

Then tried the trick of starting the search, then adding the new device in harmony where it will then try to pair the PS3 for the first time already when Remotebuddy is searching, again nothing could be found........

Really appreciate the help, however doesn't seem to have fixed it yet.

Any other ideas?

Thanks.

Okay this has been fixed...... incredibly in a bizarre way.

Basically when you asked me to debug the bluetooth, it brings up the MAC bluetooth finder, I left that window on the desktop and never bothered to close it.

So today I switched on my MAC and it has "bluetooth remote" listed, so I clicked pair, it successfully paired.

Then I went to my harmony and clicked the PS3 again and it came up to pair, so clicked pair and guess what success, however Remote Buddy still did not work.

I then loaded the remote buddy wizard and scanned for remote, to my surprised it found it added it and guess what....

IT WORKS!

No idea how my MAC found the remote when it was even in pair mode, my harmony was actually watching SKY (Cable) so not even using the bluetooth feature and last time I tried to even pair was 4pm yesterday!