Try the following:
1) Note the IP address of the VM where FLR is not connecting.
2) Open a web browser to go to the vCenter's Managed Object browser (https://<vCenter IP Address>/mob)
3) Click on the following hyperlinks :
3a ) content
3b ) SearchIndex
3c ) FindAllByIp
The last hyperlink should open another pop up window (SearchIndex : FindAllByIp)
In this new window, there are three fields - datacenter, ip and vmSearch.
4) Clear out the XML value in the datacenter field. I always highlight the XML and hit the Delete key, as hitting the space key will not leave it blank, but instead with a space, and that is misinterpretted sometimes.
5) In the IP field, enter the IP address of the VM where FLR is not finding it.
6) in the vmSearch field, type the value 'true'
7) Click on the "Invoke Method" hyperlink
This should open a box beneath the hyperlink (Method Invocation Result) where the 'val' field will show the names of the VM's with this IP address.
If multiple VM's are returned, that is your problem.
If a single VM is returned, then click on the hyperlink to take you to the VM and continue with step 8.
8) Click on the config hyperlink.
9) On the VirtualMachineConfigInfo page, find the 'instance uuid' and note it.
10) Open an SSH or Putty session to the VDP
11) Run the command 'mccli dump clientcache > cc.txt'
12) View the cc.txt file, and look for the name of the VM returned in step 7 above.
If you do not find the VM in the list, then the VM has not been backed up by the VDP, and this is why FLR will not connect. Run a backup of the VM and once that is complete, try again.
A 'normal' entry for the VM will look something like :
/vCenter/VirtualMachines/Win2008R2-GS01_UCDsdCa3U3WW3iJ2YzHs0Q
fc6a9b5da90ba9ec259cf9980cc87652c6504d66
type: VMACHINE
vc_cid: 83b37ced5f59d8b88d36784947f10ed7bd823395
vm name: Win2008R2-GS01
instanceUuid: 5020ec74-26b7-5375-96de-22766331ecd1
Compare the instanceUuid value from the above file to that noted in the Windows vCenter.
12) If the instanceUuid values are not the same, then try running the command "mcserver.sh --restart". After this completes, try FLR again.
13) If the above does not resolve the issue, then it would make the most sense to open an SR with VMware support.