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At this moment the changes to the CSS are generally not supported. These may change during the upgrades to the next versions and thus not advisable to be customized.
What we currently support:
Changing the Logo (top left corner of Connect instance)
To change the default “Alteryx Connect” logo at top left, as an Administrator, open attachments under the vertical ellipses icon at top right, and upload your logo with file name “instance-logo.png” and size 200 x 33 pixels. Flush browser cache to see the change (CTRL + F5)
Changing other icons
Navigate to a specific asset, click “Edit” as an Admin, and use the “Advanced Options” section to upload a new icon image
Changing the name of the site
In the Admin panel, modify the aesthetic site name via admin -> Connect Configuration > Instance Settings