FlexDeploy enables you to modify a pipeline while a pipeline is execution a release. The changes will be picked up once the pipeline starts the next step. Changes to the currently execution step will not be picked up immediately. Keep in mind that a pipeline can be used by multiple releases, any changes will apply to all releases associated to the pipeline.
The pipeline does its best to manage different changes, but there are some changes you may be better off pausing the releases tied to the pipeline and insuring the stage you plan to change is not executing. Adding and updating stages or steps is safe. Deleting Stages or Steps or re-sequencing steps or stages with an executing release requires more awareness. If a currently execution step or stage is deleted, the execution will fail. If the Snapshot still needs to be deployed, the stage can be replayed.