When performing offline upgrades or similar operations using Daybreak, there is a certain probability that such issues may occur. It is recommended that you export your save data using the Nxnandmanager program and then recreate the virtual system.
You can use the option in hekate_ipl.ini autoboot to choose the system which you want. This is the description of the autoboot in hekate offical website.
Config option
Description
autoboot=0
0: Disable, #: Boot entry number to auto boot.