There exists a popular 2 byte corruption on the Scanalyzer disk, in the Disk "Scanner" file, and as a result, many file versions of SCANNER are infected. The problem is a pair of No-Op "$EA $EA" near the beginning of the file, these were written by mistake by some cracker (even tho the Scanner file doesn't need any crack) obvious mistake because each byte $EA overlaps partial not whole instructions, corrupting the execution if it got to this point.
Instead of $EA $EA near the start (at memory addresses $265E, $265F) it should be $C3 $20 because I located a precorruption copy. The surrounding bytes form this string: $"85 C3 20 16 27" which has STA and JSR instrs.
Doing better after making a new disk with a Fresh install of DOS 2.5, had come with some corrupt bits in the DOS.SYS file, made directory printouts report errors.
For a real life case of the hidden directory trick, check out the APX game disk #20050 "Eastern Front 1941" the 1981 version not the 1982 Atari version. Scanalyzer, though clunky, defeats this game disk's hidden directory.
This is a collection of six (6) low level hacker utilities, all written in compiled BASIC not ml as mentioned. #1 can remove the hide feature of getting a LIST from a BASIC program. #2 searches disks for hidden directories. #3 makes cartridge dumps (they say to "TILT TO THE RIGHT SLIGHTLY" giggle). #4 is a disk utility sector editor can report bad sectors and map the vtoc. #5 is a typical disassembler. #6 is a disk backup utility that tried copying bad sectors by writing newly formed bad sectors in two possible ways, more giggles. You could try making your own bad sectors either by wobbling the rotation speed of the drive motor during write, or by wiggling the disk itself during write. They had you make two handles on the disk with adhesive tape, "can take up to 10 minutes per sector", it's all found in the instructional PDF here.
The Scanalyzer disk itself came protected, even though it is a collection of DOS files, there is a menu program which must be named AUTORUN.SYS and the utilities can only be launched from their menu, with the one exception of the Disk Utility sector editor named "SCANNER" it can be extracted and run without DOS ! The cartridge dumper is the only one built in to the menu program, the rest come as files that can't be extracted.
This poses a problem in running these utilities mainly because they were originally written for DOS 2.0, then only PARTIALLY updated for DOS 2.5 . It matters whether the disk starts booting on DOS.SYS v2.0 versus v2.5 , some things only function one way and depending whether the disk you are examining is 2.0 or 2.5 you end up needing to boot the Scanalyzer both ways, on a 2.0 disk and on a 2.5 disk. This is in spite on the title page announcing DOS 2.5 compatibility. The Scanalyzer's protection must be removed so its two disks can be made, protection gets removed by inserting these 7 bytes at the head of the autorun.sys file: "FF FF FF 06 FF 06 08" so that file grows 7 bytes in size. Then AUTORUN.SYS can be copied to any DOS.SYS version on any blank disk, and the other files moved there also.