My site is running on Joomla 3.9.3 using the Joomlart template, JA City Guide 1.0.2.
I just completed my site, upon migrating to the actual server, the module positions in the Layout tab in Template Manager longer appears.

I have two test sites, both are working fine (ie with the module positions in the Layout tab intact). Here are the systems information:
TEST SITE ONE
http://mediagenesis.com.sg/felicita/ (VPS):-
Database Version: 5.6.33
Database Collation: utf8_general_ci
Database Connection Collation: utf8mb4_general_ci
PHP Version: 5.6.39
Web Server: Apache
WebServer to PHP Interface: cgi-fcgi
My first test migration works:
TEST SITE TWO (cloned from TEST SITE ONE)
http://mediagenesis.org/felicita/ (VPS):-
Database Version: 5.6.36-82.1-log
Database Collation: utf8_general_ci
Database Connection Collation: utf8mb4_general_ci
PHP Version: 5.6.40
Web Server: Apache/2.4.29 (Unix) mod_hive/6.25 OpenSSL/1.0.1e-fips mod_fastcgi/2.4.6
WebServer to PHP Interface: cgi-fcgi
However, on the actual server where it is supposed to run, I found that module positions under the Layout tab no longer show. This is the systems info of the actual server:
LIVE SITE
http://felicitasglobal.com/index.php:-
Database Version: 5.6.43
Database Collation: utf8_general_ci
Database Connection Collation: utf8mb4_general_ci
PHP Version: 5.6.40
Web Server: Apache
WebServer to PHP Interface: cgi-fcgi
Not sure if this is related to the missing Layout issue, but I have noticed certain peculiar things as well. For example the different bootstrap classes are are on tests / live sites for the same object. For example, on the test sites:

the site on the actual server shows this. This causes some formatting issues.
