Library scan "loses" media, metadata refresh "finds" it again

I experienced the same problem and for me, too, only one library (the first that was created when my PMS was set up) was affected.
It has to do with caching information for SMB connections. In the thread linked by @Atomatth you will find the workaround to disable caching in the nsmb.conf file.
However, for me enabling the SMB3 directoy leasing option in the Advanced Setting of the Synology solved the problem (here)

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