What are the side effects of changing MySQL `character_set_server`? I am having some strange issues with character sets on my system. After digging through all kinds of settings, I found a discrepancy in my character set settings. 

When I run show variables like 'char%'; I get: 

+--------------------------+----------------------------+
| Variable_name            | Value                      |
+--------------------------+----------------------------+
| character_set_client     | utf8                       |
| character_set_connection | utf8                       |
| character_set_database   | utf8                       |
| character_set_filesystem | binary                     |
| character_set_results    | utf8                       |
| character_set_server     | latin1                     |
| character_set_system     | utf8                       |
| character_sets_dir       | /usr/share/mysql/charsets/ |
+--------------------------+----------------------------+



Are there any side effects to changing the the character_set_server variable? 


Could it possibly affect what character set a connection will use when talking with the database?
Could it possibly alter the existing data in any way? 



From my understanding, it looks like all it does is set the character set for you when creating a new database if you don't specify a charset. Is that really all it does? 

Source: https://www.blueboxcloud.com/insight/blog-article/getting-out-of-mysql-character-set-hell
You've stumbled onto one of the imponderables of MySQL's default configuration. To quote from the documentation on Character Set Configuration:


  ...when character_set_system differs from character_set_server or
  character_set_client, and you input characters manually (as database
  object identifiers, column values, or both), these may be displayed
  incorrectly in output from the client or the output itself may be
  formatted incorrectly. In such cases, starting the mysql client with
  --default-character-set=system_character_set—that is, setting the client character set to match the system character set—should fix the
  problem.


To distill, not changing the value of character_set_server will almost certainly eventually cause you problems if you use Unicode characters outside the base ISO-latin-1 character set.