Truncate can only remove free space from the end of the file.
Compact is asking how much free space do you want at the end of the file.
The free space is likely not evenly distributed.
I mostly used the ^DATABASE utility.

It looks like you are missing the kill to cleanup.

kill ^IRIS.TempIntegrityOutput(+$job)

Something to know is you can pass a routine to IRIS but not a set.  Look at the iris terminal options here.

As a guess the shell is interpreting $job rather than passing it to IRIS.

try this

echo 'set sc=$$CheckList^Integrity(,,,,5) do Display^Integrity() kill ^IRIS.TempIntegrityOutput(+$job)' | iris session [INSTANCE] -U %sys

one issue with this approach is you need to get the same IRIS session that the integrity check ran in.

An instance name is not guarantied to be unique.
hostname/ip + instance is.
For example the instance name of our failover primary and backup is the same they are just on different hosts.
We use DNS name not IP addresses though so we have DNS/instance for SystemName.

Mirroring Configurations within a Single Data Center, Computer Room, or Campus

I would ask your vendor what they develop on so you don't have to listen to an excuse around a support issue.

I would check that your iris.key file exists and has not expired.

Not sure where messages.log is on Windows but I would look at that over a Windows log.

Guessing the upgrade did iris start [instance] nostu to not run any user code on startup.
iris help start
                            **** iris usage ****
Syntax:
        iris start <instance name> [parameters]
Description:
        Run the instance's irisstart procedure to bring InterSystems IRIS up.
Optional parameters:
        quietly -> non-interactive, with minimal dialog
        nostu   -> don't run startup routine (^STU)
        help    -> list supported parameters
        EmergencyId=username,password -> start up in emergency mode
        Any other value is taken as a configuration file name with '.cpf' appended.
        If a configuration file is not specified, the file 'iris.cpf' is used.
Example:
        iris start mystuff quietly      <- uses file 'mystuff.cpf'
Notes:
        Some instances might not have support for a particular parameter,
        or a new parameter could have been added.  For a list of supported
        parameters for a specific instance, type:
                iris start <instance name> help

Looks like :Aliases were added IRIS 2021.1 - Aliases

I would not completely replace users with LDAP.

Database owner and admin should be local to the system.

Make sure your LDAP source is not a single server.

The recommendation is XFS from Supported File Systems.

The irisstat command with the -u option allows you to look at this without going into iris.

You can also look at locks in the portal - Monitoring Locks

I had to debug an application LDAP issue and I used to Apache Directory Studio.

It turned out that the user had been copied from one OU to another and not moved.

Can you login with iris session [instance] -U %sys?

From there you can use ^SECURITY to change the password.

One thing to check is use a text editor to make sure your keyboard is working by typing the password.

Not sure that you have seen that Intersystems deprecated SAM November 13th.