Thanks for the logs.
It seems to be a bug in the server. Combined with this change in WinSCP that is meant as a workaround against common bugs in SFTP server:
Issue 2247 – Limiting SFTP version to 3 with non-well-known SFTP servers as a workaround for interoperability issues
SFTP protocol versions higher than 3 are rarely supported, hence badly tested and commonly buggy. For this reason WinSCP in recent versions do not employ never SFTP servers with less known servers. But your server actually seems to have the appending correctly implemented in SFTP version 5 (used by older versions of WinSCP), but has it broken in SFTP version 3 (used by the latest version of WinSCP).
You can "fix" that by forcing WinSCP to use SFTP version 5:
sessionOptions.AddRawSettings("SFTPMaxVersion", "5");