I have the same problem when I sync across multiple instances of Logseq. It started happening after I enabled the beta smart merge which I had enabled because some content was disappearing otherwise.
I haven’t investigated deeply but I believe it may be related to having various line endings in your graph. Windows stores EOL as CRLF while Linux stores them as LF only. This means that a line might look the same but be considered different by Logseq based on the line endings.
I am using git version control which is helpful to find those problems and roll the changes back but I believe it may also be the cause of my problems.