Your nightly build version is rather old. Commit 9f18fee124 is from 10 weeks ago. So i would guess that an update to the current nightly build might fix your issue (meaning there is a chance that the bug that resulted in library corruption is no longer present, I do not assume that your symbols will be repaired automatically). You might however still want to report this issue as library corruption would be a rather serious issue (search first if something like this is already reported and possibly closed)
Just in case you are unaware: 5.99 versions of kicad are the nightly builds not stable releases. These are development snapshots that are build every night and are therefore rather unstable. They are meant to give users a relatively easy way to help test future releases.
For more details see see Is it a good idea to use a nightly build version?
In case you were unaware that these are nightly builds and are now wondering what to do: Well your current projects can not be opened in the stable version. Meaning you will need to stay with nightlies at least for them. And as v6 comes closer it might even be preferential to completely stay with nightlies until it is finally released (as your libraries are now also in the new file format so going back is possibly quite a lot of work).
However, as there will be another version 5.1 release soon i doubt that v6 is really this near so who knows what the best long term option for you will be.