Good morning. As I look back over your post, I'm not entirely sure I see what's wrong.
When I run the same commands in a sandbox lab, I get the expected results, shown below, redacted. You can see the LIF migrated nodes correctly.
PS C:\Users\BINGEN> Connect-NcController <my IP>
Name Address Vserver Version
---- ------- ------- -------
<IP> <IP> NetApp Release 8.3.1: Mon Aug 31 12:42:08 UTC 2015
PS C:\Users\BINGEN> Get-NcNode
Node NodeModel NodeLocation IsAllFlashOptimized
---- --------- ------------ -------------------
<node>-10 FAS3250 <location> False
<node>-11 FAS3250 <location> False
PS C:\Users\BINGEN> Get-NcNetInterface
InterfaceName OpStatus DataProtocols FirewallPolicy Vserver Address
------------- -------- ------------- -------------- ------- -------
<node>-10_clus1 up Cluster <IP>
<node>-10_clus2 up Cluster <IP>
<node>-11_clus1 up Cluster <IP>
<node>-11_clus2 up Cluster <IP>
cluster_mgmt up mgmt <cluster> <IP>
<node>-10_mgmt1 up mgmt <cluster> <IP>
<node>-11_mgmt1 up mgmt <cluster> <IP>
lif1 up {nfs, cifs, fcache} data svm1 <IP>
lif1 up {nfs, cifs} data svm2 <IP>
PS C:\Users\BINGEN> Get-NcNetInterface | select InterfaceName,HomeNode
InterfaceName HomeNode
------------- --------
<node>-10_clus1 fas3250-rtp-10
<node>-10_clus2 fas3250-rtp-10
<node>-11_clus1 fas3250-rtp-11
<node>-11_clus2 fas3250-rtp-11
cluster_mgmt <node>-10
<node>-10_mgmt1 <node>-10
<node>-11_mgmt1 <node>-11
lif1 <node>-11
lif1 <node>-11
PS C:\Users\BINGEN> Set-NcNetInterface -Vserver svm2 -Name lif1 -HomeNode <node>-10
InterfaceName OpStatus DataProtocols FirewallPolicy Vserver Address
------------- -------- ------------- -------------- ------- -------
lif1 up {nfs, cifs, fcache} data svm1 <IP>
lif1 up {nfs, cifs} data svm2 <IP>
PS C:\Users\BINGEN> Get-NcNetInterface | select InterfaceName,HomeNode
InterfaceName HomeNode
------------- --------
<node>-10_clus1 <node>-10
<node>-10_clus2 <node>-10
<node>-11_clus1 <node>-11
<node>-11_clus2 <node>-11
cluster_mgmt <node>-10
<node>-10_mgmt1 <node>-10
<node>-11_mgmt1 <node>-11
lif1 <node>-11
lif1 <node>-10