Even after manually Deactivating a Niagara component, this Niagara component may be revived under certain conditions. This issue occurs when the following conditions are met before the Deactivated Niagara instance is in the Complete state
After this, the Niagara system is respawned when the scalability settings meet the conditions to respawn a Niagara system.
An example of the scalability settings that easily reproduce this edge case is as follows;
I attached a repro project (FXIssueUE53.zip). Please use it. Otherwise, read the description and prepare another repro project.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-198200 in the post.