So i spawned out some bases from blueprint and done some digging then logged out when i came back they were like this the markers are there but no bases I restarted the server turned off all mods and restored the default config file this is not the first time this has happened .
that sounds as if a pretty old bug from A8.2 has re-emerged.... If such thing happens a second time, and therefore repeatable in some way, you should save the game and file a Bug report so the Devs can look into it and find a proper Solution
This sounds identical to a bug report that was already started, https://empyriononline.com/threads/entire-structures-missing-on-entry-into-game.48734/ Please add your findings there too to help properly track this issue.
I will note that some entities are disappearing like that. I believe it to be a cache issue not properly updating, as I see this with a variety of scnearios (SVs dock/undocking, combat, etc...). A potential workaround is to restart your client, wiping your client's cache*. *will delete readied blueprints