If you have a 24/7 system, you have no choice but running index rebuild on the system while it is live.

But there is very much which is unclear in your posts. You enabled TDE, and for some reason you seem to think the system took a performance hit because of this. And then you start to talk about index rebuilds, although we have told you that TDE does not cause fragmentation.

Without knowing much about your system I can only offer wild guesses. Since you talked about restrarting SQL Server when disabling TDE, should I infer that you restarted SQL Server after enabling TDE? Since this flushed the plan cache, maybe you got some bad executions plans because statistics were out of date?

What does "SELECT @@version" return?