When the software goes to save the file to the drive, it looks to see if there is a file by that name already, and if so, it will ask if you want to keep both (usually) and if you say yes, will adopt the numbering structure. So, if you scan 5 documents on Monday, they should be named Scan, Scan (1), Scan (2), Scan (3) and Scan (4). Then if you scan two more on Tuesday, they should be named Scan (5) and Scan (6) IF YOU DID NOT MOVE OR RENAME THE FILES YOU SCANNED ON MONDAY. Yes, that was for emphasis. The numbering does NOT come from the scan software, it comes from the file saving process and only works if there is a name conflict where you want to save. Frankly, it's a bit of a trick and not how the scan software is designed. As far as the scan software is concerned, it's naming the files all "Scan" but the OS is not allowing the overwriting (because you said not to do that), so the OS is renaming the files with numbers to keep them separate. The scan software is unaware of what the OS is doing.
But the multipage process is INTERNAL to the scanner. So if you scan the same five files on Monday, then on Tuesday want to scan into a multipage document with the same name, the scan software opens the "Scan" document (assuming that's the name you gave for this multipage document) and then puts the new images into that file, just as you asked. If "Scan" already exists, the scan software opens it and adds the new pages, as you said to do. But what you WANTED was to have those new images in a separate file, which requires that you now create a new name, let's say "ScanMultiple" and put the multiple images into that document instead of adding them to Scan. The OS doesn't renumber this document because it has been properly opened and then saved back with the same name, so no name conflict.
You are asking the software to read your mind about what you want it to do, which it clearly cannot do. You have to be explicit in telling it what to do with the images it scans. That's just how it works. The trick of letting the system renumber them is a hack, and it works reasonably well, as long as you don't move the previous files away. If you move or rename them, there is no name conflict and the trick doesn't work.
I don't know exactly what you are trying to accomplish another trick you can play is to set the scan name to the date of the scan, for example, 2020-10-10 for today and then let the OS add the numbers so you end up with 2020-10-10 (2), 2020-10-10 (3) etc. Tomorrow you would change the name to be 2020-10-11 and end up with 2020-10-11, 2020-10-11 (2), etc. The good news here is a sort by filename will sort them to scanned order, if that is important to you.