I have started afresh.
It would be useful to learn if Favourites can be captured from earlier installations.
Regards
G

I am attempting to get out of trouble after having had several problems with Hardware-Software combos. Cookie has been caught up in the ensuing mess. At some point in the Reinstallation or Restoring of macOS, unnoticed because my focus was elsewhere, Cookie became separated from the Favourites List.
Q 1. Is it possible to salvage Itjhr Favourites List from an earlier OS Drive?

Reading about the requirements to enable Cookie and Safari to function together I think all the directions were duly followed but:

~/Library/Application Scripts/com.sweetpproductions.Cookie5/

cannot be found. There seemed little harm in trying so this Folder was created and the 3 Files generated during the process were placed inside it. This has not helped the situation.
On an earlier revisit of my unlocked OS Drive, adding Cookie to 'Accessibility' mentioned below, along with the Folder creation above, did not resolve the problem.
Q 2. I was unable to find the 'Full Permissions' window/field/area and assumed:

System Preferences > Security & Privacy > Privacy > Accessibility

was the same place by a different name?

I also discovered that the OS Drive in use will not allow me to access:

System Preferences > Security & Privacy > Privacy > Accessibility

so that Cookie can be added and provided with essential permissions.
This is due to the installation of a YubiKey and seems to be part of the Yubico Self Preservation Society, in that it is determined not to leave any back doors open that could allow the protection to be defeated.
I have another similar OS Drive that is not, yet, YubiKey protected and this could be utilised to help resolve this if there is nil alternative solution.
Q 3. Is there anything toward getting Cookie fully operational on the 'locked' drive or is it essential for me to abandon it and set up the unlocked drive?

Q 4. Lastly is it likely that a reinstallation of Cookie will resolve this problem?

Any help very welcome, thank you.

Best regards, G

My setup is Mac OSX El Capitan v 10.11.6 with Safari v 11.0 (11604.1.38.1.7).
The website in question appears to be properly set up in Safari with regard to cookies, and Safari > Preferences > Privacy is set to 'Allow cookies from websites that I visit'.

I have been successfully using Cookie for a long time and the website in question has been accessed very regularly without any problem.
The number of Favourite websites has remained around the figure currently showing for some time.

I am not aware of removing the website in question but it has disappeared from my list of Favourites. The problem came to light about a month ago when I experienced having to Log In every time I moved between areas of the website.

Normally when visiting a website Cookie includes it within the listing giving the user an opportunity to mark it as a Favourite. 
In this case whilst the website is being used the listing fails to show that it is present and so it is not possible to mark it as a Favourite.

Being 'Logged Out' every time the user browses another page is frustrating.
However after one re-log on the website details appeared in Cookie very briefly but I was not quick enough to be able to checkmark the Favourites box.

Any help you can give will be greatly appreciated.

That 'workaround' was great, thank you.

In case it is any help the Console output with Cookie Filter is:

29/07/2016 03:45:43.566 sandboxd[137]: ([6610]) Cookie(6610) deny file-read-data /Users/StanzPro/Library/Safari/Databases/___IndexedDB
29/07/2016 03:45:43.573 sandboxd[137]: ([6610]) Cookie(6610) deny file-read-data /Users/StanzPro/Library/Safari/LocalStorage
29/07/2016 03:45:43.579 sandboxd[137]: ([6610]) Cookie(6610) deny file-read-data /Users/StanzPro/Library/Safari/LocalStorage
29/07/2016 03:45:43.000 kernel[0]: Sandbox: Cookie(6610) deny(1) file-read-data /Users/StanzPro/Library/Cookies

To my untrained eye this looks VERY similar to the previous output.

Filtering 'All Messages' using 'Cookie' produces a lot of info.

This Reply will not accept the intended attachment:

Messages Filtered by 'Cookie'.log

How should I proceed ?

Sorry, I should have said 'A couple of sessions later......' NOT '...days later...'

However Cookie just automatically offered the Update again, but still the installation fails.

The UpDate commenced automatically but resulted in a failure to install.

A couple of days later it was initiated manually with a similar result.

Is it my system or is there a problem with Cookie?

The issue you mentioned is probably why I missed 3.3.3, too busy at the time to resolve it but that is water under the bridge now.

Updating from the download Link you provided worked like a charm, thank you.
Best wishes,

G

Tried several times now, automatically when offered the Update, and manually within Cookie.
Download takes place - Extracting commences - Cookie crashes.

Report attached as PDF.

Regards

I have searched for other instances of this problem but cannot locate any Threads or Posts.

This loss of the Cookie Icon from the Menu Bar may be an Onyx problem, but no other Menu Bar items are affected?

My Mac Pro [Early 2008] is different to normal in that it is running Mavericks from an External RAID 0 at SATA 3 rate, and the problem may have surfaced at the time this Hardware was set up.