Hi @UğurcanGül,
I faced the same issue before. All the content of ArcGIS Portal disappeared after restarting the machine that hosted the Enterprise components and when I tried to create items using the same name of one of the items that existed, the portal told me this item already exists.
What I did to solve this was to reindex the Portal content.
Portaladmin\System\Indexer\ReIndex.
After the reindexing process, all the items were back and worked properly.
But I didn't have any space issues.
I hope that this could help.