If it gets deleted, it's probably because you are not using the official extractors for that version. The "VMap file './vmaps/000.vmtree' does not exist" also means it can't read the file, due to unsupported version.
You have to extract them fresh from what you compiled. Do NOT download and use unsupported mmaps, dbcs, or vmaps from another source.
https://trinitycore.atlassian.net/wiki/spaces/tc/pages/2130046/Server+Setup#ServerSetup-Extractors