Team Fortress 2 Classified requires additional configuration for Sourcemod/Metamod support. This extra configuration gets wiped with updates.

[MoiraPrime]

This mod requires some extra configuration to work with Sourcemod. These changes get wiped whenever you update the mod. The documentation for these additional configurations can be found here: https://wiki.tf2classified.com/wiki/Dedicated_Linux_server#Installing_SourceMod

[IceOfWraith]

There's a setting called Validate SteamCMD Downloads that you can turn off if it's the actual Steam downloaded file that gets overwritten. Otherwise, if you say which file gets replaced I can look closer.