I don't think it is quite an accurate description of what happened.
"Arduino AVR Boards" platform locations for Arduino IDE 1.x
In order to allow users to get started quickly with the minimum of complexity, the Arduino IDE 1.x installation comes with a bundled copy of the "Arduino AVR Boards" platform, at this location:
However, Arduino IDE 1.x also allows you to update to other versions of "Arduino AVR Boards" via Boards Manager. When you do that, the platform is installed under this path:
C:\Users\<username>\AppData\Local\Arduino15\packages\arduino
If an installation of "Arduino AVR Boards" is present in that location, Arduino IDE 1.x will use it instead of the copy of "Arduino AVR Boards" bundled with the IDE installation.
"Arduino AVR Boards" platform installation by Arduino IDE 2.x
The Arduino IDE 2.x installation does not include a copy of "Arduino AVR Boards". Instead it uses the Boards Manager infrastructure to automatically install the latest version the first time you start Arduino IDE 2.x after a fresh installation. As with Arduino IDE 1.x, this installation is made under:
C:\Users\<username>\AppData\Local\Arduino15\packages\arduino
So installation of Arduino IDE 2.x will result in a global update of "Arduino AVR Boards", but this isn't caused by any change to settings. In fact, completely separate files are used for storing the settings of each IDE so you can change the preferences in one IDE without it affecting the other.
The discontinuation of recognition of the custom modification you made to "Arduino AVR Boards" would have also occurred if you updated "Arduino AVR Boards" in the Arduino IDE 1.x Boards Manager.
Independent platform
The best practices approach would be to put the custom board definition in a dedicated boards platform. This would allow updates of "Arduino AVR Boards" to be made without any impact on the custom board platform. The Arduino boards platform system allows referencing resources from other platforms, so a custom boards platform for this board definition can be as simple as a single boards.txt file in any appropriate folder under your sketchbook.
If you are interested in doing that, we can provide more information.
Isolating Arduino IDE 1.x
It is possible to completely isolate the two Arduino IDE installations so that operations performed in one IDE will not affect the other.
The easiest way to accomplish this is to put Arduino IDE 1.x in portable mode:
this will cause Arduino IDE to no longer use the files under this location:
C:\Users\<username>\AppData\Local\Arduino15
It will instead use the portable subfolder of the Arduino IDE installation folder.