I am running Windows Server 2012 and Citrix XenDesktop/XenApp 7.9. I can customize the "Default Tools" on my Acrobat toolbar and those changes with stay put between program openings, so long as it is either launched through StoreFront or by double-clicking a PDF in File Explorer.
I've verified this issue with many different users, all experiencing the same problem. I've found that I can create a named copy of my default toolbar so that during an Outlook-opened PDF I can just click on the Customize drop-down and select that named copy. Choosing the named copy on a File Explorer opened PDF will see that change stick without issue between opens, except for when launching one from Outlook. I am not having this issue in our older Windows Server 2008R2 and Office 2007 environment. Per the below-mentioned thread my environment is completely updated, Windows, Office, and Adobe patches and updates. I've also repaired both Office and Acrobat in TS installation mode just to be sure.
There is another thread from a different user that didn't gain any traction. I am hoping that by better explaining my issue I can get some assistance.