[jaycm8]

When I delete LinkedIn messages from my phone, they also get deleted from my LinkedIn mailbox. This is the only mailbox (amongst my email accounts, Twitter, etc) where this happens - I also prompt myself with the "hub and server" warning for all of my other ones as well. Is there a setting for LinkedIn emails where I can just delete them from my hub/phone?

[Ecm]

First off, welcome to CrackBerry!
Please update your profile to include device, carrier, and location. This makes it easier for others to help you.

I may be incorrect, but I believe that LinkedIn does not support this on the server side. It's a 2-way sync, so actions on device also apply to the server.

[Chanlion]

Think of the Hub as an extension of the app. Which makes it nice so you don't have delete stupid messages twice.
Or you can hide all Linked or certain app notifications all together from the hub. Go into the hub, settings in side menu, hub management and select whatever account you want to edit.

As for why it's doing it just for one app, it should delete on both for all apps.