How to refresh a java application after making a file change

This may sounds like a dumb question to some, but I am not a Java developer, we have moved a Java app from Rackspace server to AWS linux server and upgraded MySql from 5.2.x to 5.7.x. Some SQL statements are causing issues so I am trying to fix those inside the .java files. However, when I save the file, and use .sftp library from VSCode to push the changes to the linux server, then refresh the site, it does not reflect the changes. Is there anything else I need to be doing every time I make a change?
I was able to update some string in a .jsp file and that worked when I refreshed, so I am not sure why when I change a .java file, it does not reflect change.

The entire directory is confusing to me, I believe it was done so that all files, configs, tomcat files, etc. would be under one git folder so that it can just be dropped anywhere. I find a lot of sources state that a .war file would be created and you would place that file in the tomcat apps directory.

Here is the basic layout of the directory of the app

-www/live/njun
 -build.xml
 +lib
 +scripts
 +sql
 +src
 -tomcat(has some config files, scripts, webapps folder)
 -web  
   -content
   -index.jsp
   -trampoline
     -includes folders with .java files
     -tickets
      -ticketsMgr.java (this is the file I modified but I could not see any differences in app)
     -index.jsp (this is one I modified and did reflect in browser)
   -WEB-INF
     -classes/com/njun
       -lots of folder that have .Class files(although when I open them it's all gibberish characters)

This is the basic structure of what I am looking at.

I tried going to the /opt/tomcat/bin and > sh startup.sh - to restart tomcat. That didn't work.

I also ran the > sh startup.sh version inside of the tomcat folder above,
/tomcat/bin/sh startup.sh - that shows me some info where the home, base tmpdir, jre_home, etc. But that didn't work neither.

I am not being asked to make major modifications on this app, I figure I can manage the SQL errors myself. If we get to the point where we need enhancements done to this app, we would hire a Java developer.

Please let me know if I am missing something and I can provide.

Thanks in advance,

That's because a .java file is just source code. You need to compile it and upload the corresponding .class file generated when you compile the .java sources. How to compile and run a Java program. Or well, since it runs on a Tomcat instance, you might have a JAR or WAR file. But the idea is still the same, since those are just basically zip files that hold your .class files (among other stuff that's less relevant for your issue).