Hey Apostolis,
Thankfully it looks like the error is telling us exactly what's happening (seems rare we get that luxury haha) but the question is why can't you get a lock on it (presumably something already has it locked). I assume these VMs are all part of the same Linked Clone pool. If so, can you recompose that pool?
If I'm not mistaken recomposing should recreate the descriptor (the -checkpoint.vmdk file) if you recompose the entire pool or switch parents. It might only be on parent change though, can't remember for sure. To that end, if that doesn't do the trick or you can't recompose, try creating a new Linked Clone pool to mimic that one (maybe 2 VMs initially) and test those out.
~Brandit