Operational file save issue starting from v 0.28.1

[AugustinVintzileos]

As of v0.28.1 there is a problem in saving the operational files. Chain of actions:
(1) load ascii.out file
(2) generate tree not using all variables in ascii.out
(3) save breakpoints
(4) re-load breakpoints
(5) delete variables that were not used for the tree in he list of variables
(6) save operational files

ERROR->
(500) POST /postprocessing/save: ValueError: Shape of passed values is (56, 100), indices imply (46, 100)