Bash – HISTSIZE not being set in bash

The problem actually boils down to the different behavior of login and non-login shells. I had set the variables that control history in my ~/.bahsrc. This file is not read when one starts a login shell, it's only read by interactive, non-login shells (from man bash):

When bash is invoked as an interactive login shell, or as a non-interactive shell with the --login option, it first reads and executes commands from the file /etc/profile, if that file exists. After reading that file, it looks for ~/.bash_profile, ~/.bash_login, and ~/.profile, in that order, and reads and executes commands from the first one that exists and is readable. The --noprofile option may be used when the shell is started to inhibit this behavior.

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When an interactive shell that is not a login shell is started, bash reads and executes commands from ~/.bashrc, if that file exists. This may be inhibited by using the --norc option. The --rcfile file option will force bash to read and execute commands from file instead of ~/.bashrc.

Therefore, each time I logged in, or dropped to a tty, or used ssh, the .history file was getting truncated because I had not set it to the right size in ~/.profile as well. I finally realized this and simply set the variables in ~/.profile where they belong, instead of ~/.bashrc

So, the reason my ~/.history was getting truncated was because I had only set the HISTORY variables in a file read by interactive, non-login shells and therefore every time I ran a different type of shell the variables would be ignored and the file would be cut accordingly.