If you have made Ventoy official partition images and switched one of them into Partition 2 using agFM then you must NOT then try to update the new Ventoy drive because this will completely format and re-write the entire contents of Partition 2 and will also overwrite the E2B backup sectors located at the start of the E2B USB drive and replace the grub4dos boot code.
This means that you cannot restore the original E2B Partition 2 or the original boot code.
The best thing to do is to backup (copy) all the contents of Partition 1 (the first NTFS partition with the payload files, etc.) and also Partition 3 if you made an extra partition and then remake the E2B USB drive using Make_E2B.exe again and copy the files back onto the USB drive.
If you wish to have the latest official Ventoy version, you must re-make the Ventoy partition images again using the \e2b\update e2b\Make_Latest_Ventoy_Partition_Image.cmd script on the second partition of the E2B USB drive.