To start, there is no problem with the USB breakout board (BOB) Mach3 100Khz 4 axis.
At the beginning, I thought so. I was starting to go crazy and checked every possible aspect of the problem:

1.) I changed the position of the encoder because I thought it may be missing steps (I also destroyed one of my encoders because I forgot to cut the power while playing around in one of the many tests).
2.) I swapped all the drivers and motors, and it was still missing steps.
3.) I thought maybe it has to do with electromagnetic interference (ChatGPT gave it as a prime suggestion), so I started to learn about electromagnetic interference and I rerouted all the wires, mainly dividing high voltage (220V) to one side of the cabinet, middle voltages (48V) in the middle and low voltages (24V, 5V) in the other side. I made sure no cable cross-talked to any other cable; I twisted the wires in order to mitigate their interaction, I also connected the sleeve of the encoder cable to the common of the drivers (it was suggested by ChatGPT and other resources online to connect it to ground, however, when I looked at the signal line with my oscilloscope, I noted that when I don't connect anything I have noise, but when I connected it to the ground the noise increased significantly!, only when I connected it to common (negative lead) of the driver the signal noise was removed completely!!!
4.) I tested the motors via RS232 with LeadShine software. There was no problem with position even if I tested it for 1,000 cycles at max speed, so I knew that it had nothing to do with the motors or the drivers.
5.) I also had this strange coincidence that Y and Z always had a shift, but the X-axis didn't have any shift, so I started to think okay if I connect a different driver and a motor to X axis will it still have a problem? From this test I was sure that it had nothing to do with the HBS57 drivers.
6.) Finally I ordered another BOB thought maybe it is a problem with my BOB, however, I already found the problem at this stage...:

After looking online at someone who changed the preferences of the computer from ACPI x64-based PC (parallel mode?) to Standard computer (serial mode?), and it fixed his problem, I thought maybe it's something to do with the software, up until this moment the only thing that I checked was hardware, I didn't realize that it could be a software problem, because I did everything exactly according to the video I saw on YouTube
LINK:
https://youtu.be/BBoTkRH2E_I?si=B3kFTEPAzgHmOdlh
and this was the problem!!!

The problem was copying the "Mach3Mill" configuration file, when you only copy the driver file "RnRMotion.dll" into the proper folder (PlugIns) there is no problem, it will run perfectly! and you will not lose any steps, even if you let it run like 10 meters in one direction at 5meters/min!!! It will be exactly where it should be (I removed the motors and marked a line on a tape relative to the coupler on the shaft), but when you copy the configuration file "Mach3Mill" to mach3 main folder you are essentially using the settings of someone else's PC instead of your own, and these settings are obviously wrong! I didn't manage to find out what exactly was misplaced in the file, I did notice that the name of the file was different in three different locations, I changed it, but it still had the same problem. The file has directories in Chinese which has nothing to do with your PC... and you don't need it anyway because when you copy "RnRMotion.dll" file it works instantly, there is no reason to take this file from someone else's computer!!!

You should instead copy the "RnRMotion.dll" configuration file to the relevant folder. Then, set up your own settings in the default Mach3Mill profile (not on a custom profile name you made!). Set your own pins for the E-stop trigger etc., including motor tuning, and all other necessary adjustments. After that, you can copy the Mach3Mill file that was created for you in the Mach3 folder and create a backup for future use. This file name can be changed and used for your custom-made profile (simply make sure you give it the same name as your profile and overwrite the file in Mach3 folder if it already exists)!

I don't know if the file shared in the video is corrupted or if some folders are missing, but you should always stick to the default folder directory for Mach3 and set up your own Mach3Mill file. The settings I currently have are attached.

I hope I was able to spare someone a week of their life, as mine was completely wasted!!!
So basically, there is no problem with the BOB at all. It can move three Nema23 servo motors simultaneously at 5000mm/min with 1000 steps per mm! This is very impressive. The only reason all of this craziness started was because the steps given in the video were misleading. I don't see any reason to pay for the expensive BOB when this little guy costs only $5 on AliExpress.