When viewing or modifying the client's server list, servers.dat is not modified/updated, but replaced with a new file.
The biggest issue that this creates is that links are replaced with real files, as the new servers.dat is a different file with a new inode.
In MC-34205, a similar issue was marked wontfix, because Java 6 could not tell a symlink from a real file. However, as Java 8 is the minimum required version as of Minecraft 1.12, there is no need to support the old code that handles servers.dat.
If code is only changed for symlinks, however, this will still cause an issue for anything that depends on the inode, such as hardlinks.
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galaxy_2alex
Please check if this still occurs in 1.16.1/20w29a - if possible, please also provide reproduction steps for the issue.
Issue updated. The most recent release and snapshot are tested and still affected. Additionally, the file is even replaced by simply viewing/loading the server list.