Hello,
We finally found the issue, since we are using some network tool for backup, while reverting the snapshot, some ID on the vmdk were still referring to the backup folder, here is an example :
[root@esxihost:/vmfs/volumes/a59a2c87-xxxxxxxx/myvirtualmachine-restored] cat myvirtualmachine-000002.vmdk
# Disk DescriptorFile
version=1
encoding="UTF-8"
CID=xxxxxxx
parentCID=8xxxxxxx
isNativeSnapshot="no"
createType="vmfsSparse"
parentFileNameHint="/vmfs/volumes/a59a2c87-xxxxxxxx/.snapshot/daily.2019-09-24_0010/myvirtualmachine/myvirtualmachine.vmdk"
# Extent description
RW xxxxxxxxxx VMFSSPARSE "myvirtualmachine-000002-delta.vmdk"
# The Disk Data Base
#DDB
ddb.longContentID = "1281b2ca1xxxxxxxxxxxxx1cbc90"
ddb.toolsVersion = "1xxxx9"
So by removing ".snapshot/daily.2019-09-24" we were finally able to consolidate the machine.
Thanks for all of your suggestion.
Josué