When you do a full flash (either OS&EMMC or just*OS) your ubiboot configuration gets wiped by the flash, no need to remove anything.

Did you get my previous reference to back-to-back flashing? that is just about the only way to enter open mode without any problems later.

The reason for that is that when a device in closed mode is opened, there are lots of places where it still has closed-mode aegis credentials used, which will not work in open mode. These are something which are created it the first boot of a fresh device and used ever after from that instant.

How to avoid this is to make sure the device never gets the chance to boot in closed mode after fresh flashing. This sounds contradictory as fresh flashing always puts the device in closed mode... but there is a fix to do it

You need to do it so;
1.) Prepare the device for fresh flashing, but also have an open mode kernel ready.
2.) When you give the command to flash the device, have either another console open waiting to flash the openmode kernel or have the command in sequence. What you want to do, is immediately enter kernel flashing command when the first flashing is done, without waiting between the commands for the device to boot up
3.) After doing this, the device boots up the first time, and already has the open-mode kernel, hence it creates all aegis keys in Open Mode and avoids all the problems described earlier