The libraries do not need some special work. (The lib file format did not change) But the schematic file needs to be remapped.
The reason for this is that version 4 did not store the information about what library a symbol was taken. This meant that symbol names needed to be unique over all libs. In version 5 the library information is included in the schematic file. (So when transitioning from version 4 to version 5 this info needs to be added.)
Normally everything should kind of happen automatically but it could be that you either found some bug or you made some mistake in that process.
The automatic process should be started the first time you open the schematic. (Something about remapping and or rescue) If this comes up accept the default values. You need to store the schematic after the remapping is done. (The file will no longer be compatible with version 4)
The remap process depends on a valid cache lib. (The cache lib is a special file that is created by kicad inside the project directory.)
There where problems reported when the project was not made by a version 4 stable release but with a nightly build.
I can not explain why adding symbols from libraries would result in them being forgotten after restarting kicad. The only thing that comes to mind is that you choose the symbol from either the cache or rescue lib. (Make sure you get the symbol from a real library)