Yeah, there are periodic updates to the Arduino AVR Boards platform and the IDE will give you a notification prompting you to update. When you do that update, the previous Boards Manager installation will be removed and any customized files in that location lost. In the case of modifying the copy in the Arduino IDE installation folder, the modified files will be lost when you update to a new version of the IDE.
The normal approach is to do library development on a copy of the library in the "libraries" subfolder of your sketchbook folder (shown in the Arduino IDE's File > Preferences > Sketchbook location preference). The sketchbook folder contents are not affected by boards platform and IDE updates.
However, this is a little bit tricky when dealing with libraries like SoftwareSerial that are normally bundled with the boards platform. The reason is that the platform bundled libraries are only accessible when compiling for a board of that platform. This allows each platform to provide its own implementation of these libraries (which are normally very architecture-specific). The APIs of the platform bundled libraries are generally all compatible, so the average user never notices that a different library is used for each board, but the low level implementation of each of those libraries might be very different. The libraries installed to the sketchbook are accessible to every board, so there is a chance that the AVR-specific SoftwareSerial library could end up being used when compiling for another board its not compatible with. The Arduino IDE does have a system for automatically picking the right library when there are multiple possible options (all the boring details here if you're interested), and will also show a message in the console that multiple libraries werefound, so in practice this is probably not a problem, but if you do that it is good to take a mental note in case you start having some strange results at some time in the future.