Previously, there was apparently a per-sub-account email address, and users could BCC the appropriate sub-account address to have an email associated with the client in that sub-account. Users with multiple sub-accounts could link to different client records depending on which BCC address they used, which provides a way for an agency employee or another third party to make sure they associated data with the right record.
Now, that feature is no longer available, and the two-way sync doesn't work when a user interacts with multiple sub-accounts. Consequently, for a situation where agency employees primarily work in an agency subaccount but sometimes need to dig into a user's mailbox for troubleshooting or such, there is now no convenient way to get email communications saved with the client record in GHL.