There were 2 ways to perform Incremental Backup of Hyper V Virtual Machine before RCT was introduced by microsoft in windows 2016 -
(Setting controlled in BE from Backup Exec global settings -> Virtual Machine section)

1) Use the standard processing method (Backup Exec Hyper V Incremental Backup Method
2) Use the faster processing method (Microsoft Incremental Backup Method)

Note: If RCT is selected and hyper v virtual machine is windows 2016 and above, RCT will be used for incremenal backup. If virtual machine is version lower than Windows 2016 then whichever option is chosen i.e. standard processing or faster processing will be used even when RCT is selected.

When standard processing method is used, the Full Backup job collects fingerprint data from Hyper V server related to Virtual Machine and stores it under Backup Exec Install Path\Data\Hyper-v folder. Backup Exec creates one folder for each Hyper-V Backup Job.This data is used by Backup Exec to perform incremental or differential backup of the Hyper-V Virtual Machines.
 

Example :

Job_Monday Backs up VM1, VM2, VM3
Job_Tuesday Backs up VM1, VM2, VM3
Job_Wednesday Backs up VM1, VM2, VM3
Job_Thursday Backs up VM1, VM2, VM3
Job_Friday Backs up VM1, VM2, VM3
 

So Job_Monday will create a Parent Folder under Backup Exec Install Path\Data\Hyper-V. Additionally there will be subfolders created for each Virtual Machine being backed up. These Folders will get overwritten when the same Job runs again.



Note: Each Job will create a Parent Folder with Unique Guid even though the same Virtual Machines is getting Backed in the other Job. 
 

This Behavior is by Design.