Coty, judging by the update you made here (where you originally raised this question as a comment one another post), for you the term "whole project" means "everything in a namespace". You have discovered that SET sc= $SYSTEM.OBJ.ExportAllClasses(filename) does what you want.

For many of us the word "project" refers to a Studio feature that allows us to group a subset of a namespace's code.

Studio projects can be manipulated programmatically using the %Studio.Project class.

Then it definitely sounds like you need to rebuild indices. After doing that, please test again without %IGNOREINDICES and let us know if the results are correct. Then test again after your application has updated records for a while. If the difference appears again, either there's a bug that InterSystems needs to know about, or perhaps your app is updating globals directly using COS commands (i.e. not via Objects or SQL).

What is your $ZVERSION value? Perhaps you are running a version with a known problem in the area of index maintenance.

Caché telnet service exists only on Windows. On other platforms would you rely on OS-level telnet service? Nowadays on UNIX/Linux it's uncommon to find telnet, and ssh is typical instead.

If there's a concern about passwords travelling in plaintext, remember Caché telnet service can be configured to accept telnet over SSL/TLS.

Vitaliy's answer pointed you to a classmethod that does the job. Sounds like maybe you're not sure how to invoke classmethods in Caché ObjectScript, so here's a transcript from a quick test run I did in Terminal:

USER>set bSame=##class(%Library.File).Compare("c:\s\junk.txt","c:\s\junk2.txt")
 
USER>write bSame
0
USER>set bSame=##class(%Library.File).Compare("c:\s\junk.txt","c:\s\junk.txt")
 
USER>write bSame
1
USER>w $zv
Cache for Windows (x86-64) 2017.1.1 (Build 111U) Wed May 17 2017 15:34:56 EDT
USER>

If Vitaliy's answer meets your needs please set the checkmark alonngside its title line.

As I understand it, the SU variant of the software is what's installed when you download from this page:

http://www.intersystems.com/library/software-downloads/

And as your error message states, this variant is barred from using a cache.key file to unlock further features.

I think you'll need a different software kit. AFAIK you'll be able to "upgrade" your current SU installation in situ without losing anything (provided you've followed the rules about how to name any of your own code that you store in %SYS).

Those of us with support accounts can download software kits via WRC Direct. But assuming you don't have such an account yet, the InterSystems folk who provided you with the evaluation key are probably the best ones to ask about how to get hold of the software kit you need.