If you are using a Persistent pendrive like Rufus makes, you can reset the drive by deleting everything on the "casper-rw" partition. Some other USB creators call this partition "writable".
The persistence file will start rebuilding itself the next boot, just like from the factory.
In Ubuntu you can make a Live, (non-persistent), pendrive using either Disks or Startup Disk Creator.
In Disks go to the upper right and select restore disk.
Select the Ubuntu ISO file as source and the USB as destination.
mkusb https://help.ubuntu.com/community/mkusb, will make anything from a Live USB to a Persistent USB with a NTFS partition so you can still use the USB for data.
You can also do a Full install of Ubuntu to USB that uses a pendrive rather than an internal disk.
You can put Kali on it's own partition if the pendrive is large enough.