Hi John_Webbo
Welcome to the communities.
Let me answer to your few question i.e
1.I'm a little confused about the different vmdk files.
Yes 000002 is working file, have you ever tried to convert vmdk to vhd in that mvmc if so then mvmc automatically create one file .
2-can I somehow get back to only using one file and free up a load of disk space ?
Please try to use front end option that is revert snap short.