Unfortunately, you cannot lock label positions in yEd.
The flowchart layout specifically always places node labels into the center of their nodes.
Currently, you only have two options:
Do not use the flowchart algorithm. You could try the hierarchic layout algorithm instead, for certain use case it produces similar results but does not necessarily change any label positions.
Correct the label positions after flowchart layout is done.
That said, it might be good idea to add an option for the flowchart algorithm that turns off node label placement. We will keep that in mind.