YES!

I deleted partition 3 and then could increase the datastore with the missing 1.8TB using vSphere Client 5.5.0-3024345.

This is the result:

/vmfs/volumes # df -h

Filesystem   Size   Used Available Use% Mounted on

VMFS-5       5.5T   2.1T      3.4T  38% /vmfs/volumes/mainstorage

vfat       249.7M 185.2M     64.5M  74% /vmfs/volumes/aeda2aeb-c934ad60-46ce-cb77abdfabaa

vfat       249.7M 182.4M     67.4M  73% /vmfs/volumes/c8ace7e9-a96a5914-16d4-a697ad4634d9

vfat       285.8M 201.6M     84.2M  71% /vmfs/volumes/55d7af6e-a25f7c97-c3ec-6805ca0de93c

I cannot explain how the partition got lost, but I read about vSphere C# Client having an issue with partitions >4TB.

Obviously this is solved with the current version. I upgraded to 5.5-U3 in the meantime.

Thank you very much!