There were realy a lot of core things that changed in version 3.0.0 (for the better of course!) and kept changing (although more minor) up to current version 3.4.2. Version 3.x was a big leap. There wer though some things that could break. From the change log online:
Breaks (sorry)
DialogueTree -> SubDialogueTree Variable Mappings will need to be re-set.
Blackboard overrides on Prefab Instances will be reverted to the Prefab Asset. (Due to new serialization to properly support Variable Overrides).
Bound Graph overrides on Prefab Instances will be reverted to the Prefab Asset. (Due to a Unity bug with [FormelySerializedAs] -> https://bit.ly/37T6CaE ). There is a way around this though. Please contact support if this is an issue for you.
Do any of these seem related to the breaks you encounter?