I tested this in 2.4.4r and was unable to replicate the issue.
I created and assigned a 3 interface LAGG and added VLANs on that using igb NICs. I edited the lagg to remove an interface and also edited the assigned lagg interface to change the MTU.
The VLANs retained their parent in each case.
lagg0: flags=8843<UP,BROADCAST,RUNNING,SIMPLEX,MULTICAST> metric 0 mtu 1500
options=6500bb<RXCSUM,TXCSUM,VLAN_MTU,VLAN_HWTAGGING,JUMBO_MTU,VLAN_HWCSUM,VLAN_HWFILTER,VLAN_HWTSO,RXCSUM_IPV6,TXCSUM_IPV6>
ether 00:08:a2:0d:16:12
inet6 fe80::208:a2ff:fe0d:1612%lagg0 prefixlen 64 scopeid 0xb
nd6 options=21<PERFORMNUD,AUTO_LINKLOCAL>
media: Ethernet autoselect
status: no carrier
groups: lagg
laggproto lacp lagghash l2,l3,l4
laggport: igb3 flags=0<>
laggport: igb4 flags=0<>
laggport: igb5 flags=0<>
lagg0.20: flags=8843<UP,BROADCAST,RUNNING,SIMPLEX,MULTICAST> metric 0 mtu 1500
options=600003<RXCSUM,TXCSUM,RXCSUM_IPV6,TXCSUM_IPV6>
ether 00:08:a2:0d:16:12
inet6 fe80::208:a2ff:fe0d:1612%lagg0.20 prefixlen 64 scopeid 0xc
nd6 options=21<PERFORMNUD,AUTO_LINKLOCAL>
media: Ethernet autoselect
status: no carrier
vlan: 20 vlanpcp: 0 parent interface: lagg0
groups: vlan
lagg0.30: flags=8843<UP,BROADCAST,RUNNING,SIMPLEX,MULTICAST> metric 0 mtu 1500
options=600003<RXCSUM,TXCSUM,RXCSUM_IPV6,TXCSUM_IPV6>
ether 00:08:a2:0d:16:12
inet6 fe80::208:a2ff:fe0d:1612%lagg0.30 prefixlen 64 scopeid 0xd
nd6 options=21<PERFORMNUD,AUTO_LINKLOCAL>
media: Ethernet autoselect
status: no carrier
vlan: 30 vlanpcp: 0 parent interface: lagg0
groups: vlan
lagg0: flags=8843<UP,BROADCAST,RUNNING,SIMPLEX,MULTICAST> metric 0 mtu 1500
options=6500bb<RXCSUM,TXCSUM,VLAN_MTU,VLAN_HWTAGGING,JUMBO_MTU,VLAN_HWCSUM,VLAN_HWFILTER,VLAN_HWTSO,RXCSUM_IPV6,TXCSUM_IPV6>
ether 00:08:a2:0d:16:12
inet6 fe80::208:a2ff:fe0d:1612%lagg0 prefixlen 64 scopeid 0xb
nd6 options=21<PERFORMNUD,AUTO_LINKLOCAL>
media: Ethernet autoselect
status: no carrier
groups: lagg
laggproto lacp lagghash l2,l3,l4
laggport: igb3 flags=0<>
laggport: igb4 flags=0<>
lagg0.20: flags=8843<UP,BROADCAST,RUNNING,SIMPLEX,MULTICAST> metric 0 mtu 1500
options=600003<RXCSUM,TXCSUM,RXCSUM_IPV6,TXCSUM_IPV6>
ether 00:08:a2:0d:16:12
inet6 fe80::208:a2ff:fe0d:1612%lagg0.20 prefixlen 64 scopeid 0xc
nd6 options=21<PERFORMNUD,AUTO_LINKLOCAL>
media: Ethernet autoselect
status: no carrier
vlan: 20 vlanpcp: 0 parent interface: lagg0
groups: vlan
lagg0.30: flags=8843<UP,BROADCAST,RUNNING,SIMPLEX,MULTICAST> metric 0 mtu 1500
options=600003<RXCSUM,TXCSUM,RXCSUM_IPV6,TXCSUM_IPV6>
ether 00:08:a2:0d:16:12
inet6 fe80::208:a2ff:fe0d:1612%lagg0.30 prefixlen 64 scopeid 0xd
nd6 options=21<PERFORMNUD,AUTO_LINKLOCAL>
media: Ethernet autoselect
status: no carrier
vlan: 30 vlanpcp: 0 parent interface: lagg0
groups: vlan
lagg0: flags=8843<UP,BROADCAST,RUNNING,SIMPLEX,MULTICAST> metric 0 mtu 5999
options=6500bb<RXCSUM,TXCSUM,VLAN_MTU,VLAN_HWTAGGING,JUMBO_MTU,VLAN_HWCSUM,VLAN_HWFILTER,VLAN_HWTSO,RXCSUM_IPV6,TXCSUM_IPV6>
ether 00:08:a2:0d:16:12
inet6 fe80::208:a2ff:fe0d:1612%lagg0 prefixlen 64 scopeid 0xb
nd6 options=21<PERFORMNUD,AUTO_LINKLOCAL>
media: Ethernet autoselect
status: no carrier
groups: lagg
laggproto lacp lagghash l2,l3,l4
laggport: igb3 flags=0<>
laggport: igb4 flags=0<>
lagg0.20: flags=8843<UP,BROADCAST,RUNNING,SIMPLEX,MULTICAST> metric 0 mtu 5999
options=600003<RXCSUM,TXCSUM,RXCSUM_IPV6,TXCSUM_IPV6>
ether 00:08:a2:0d:16:12
inet6 fe80::208:a2ff:fe0d:1612%lagg0.20 prefixlen 64 scopeid 0xc
nd6 options=21<PERFORMNUD,AUTO_LINKLOCAL>
media: Ethernet autoselect
status: no carrier
vlan: 20 vlanpcp: 0 parent interface: lagg0
groups: vlan
lagg0.30: flags=8843<UP,BROADCAST,RUNNING,SIMPLEX,MULTICAST> metric 0 mtu 5999
options=600003<RXCSUM,TXCSUM,RXCSUM_IPV6,TXCSUM_IPV6>
ether 00:08:a2:0d:16:12
inet6 fe80::208:a2ff:fe0d:1612%lagg0.30 prefixlen 64 scopeid 0xd
nd6 options=21<PERFORMNUD,AUTO_LINKLOCAL>
media: Ethernet autoselect
status: no carrier
vlan: 30 vlanpcp: 0 parent interface: lagg0
groups: vlan
I also repeated the test in hardware with em NICs with the same results:
lagg0: flags=8843<UP,BROADCAST,RUNNING,SIMPLEX,MULTICAST> metric 0 mtu 1500
options=1209b<RXCSUM,TXCSUM,VLAN_MTU,VLAN_HWTAGGING,VLAN_HWCSUM,WOL_MAGIC,VLAN_HWFILTER>
ether 00:90:7f:87:dc:78
inet6 fe80::290:7fff:fe87:dc78%lagg0 prefixlen 64 scopeid 0x12
nd6 options=21<PERFORMNUD,AUTO_LINKLOCAL>
media: Ethernet autoselect
status: no carrier
groups: lagg
laggproto lacp lagghash l2,l3,l4
laggport: em3 flags=0<>
laggport: em4 flags=0<>
laggport: em5 flags=0<>
lagg0.20: flags=8843<UP,BROADCAST,RUNNING,SIMPLEX,MULTICAST> metric 0 mtu 1500
options=3<RXCSUM,TXCSUM>
ether 00:90:7f:87:dc:78
inet6 fe80::290:7fff:fe87:dc78%lagg0.20 prefixlen 64 scopeid 0xc
nd6 options=21<PERFORMNUD,AUTO_LINKLOCAL>
media: Ethernet autoselect
status: no carrier
vlan: 20 vlanpcp: 0 parent interface: lagg0
groups: vlan
lagg0: flags=8843<UP,BROADCAST,RUNNING,SIMPLEX,MULTICAST> metric 0 mtu 9000
options=1209b<RXCSUM,TXCSUM,VLAN_MTU,VLAN_HWTAGGING,VLAN_HWCSUM,WOL_MAGIC,VLAN_HWFILTER>
ether 00:90:7f:87:dc:78
inet6 fe80::290:7fff:fe87:dc78%lagg0 prefixlen 64 scopeid 0x12
nd6 options=21<PERFORMNUD,AUTO_LINKLOCAL>
media: Ethernet autoselect
status: no carrier
groups: lagg
laggproto lacp lagghash l2,l3,l4
laggport: em3 flags=0<>
laggport: em4 flags=0<>
laggport: em5 flags=0<>
lagg0.20: flags=8843<UP,BROADCAST,RUNNING,SIMPLEX,MULTICAST> metric 0 mtu 9000
options=3<RXCSUM,TXCSUM>
ether 00:90:7f:87:dc:78
inet6 fe80::290:7fff:fe87:dc78%lagg0.20 prefixlen 64 scopeid 0xc
nd6 options=21<PERFORMNUD,AUTO_LINKLOCAL>
media: Ethernet autoselect
status: no carrier
vlan: 20 vlanpcp: 0 parent interface: lagg0
groups: vlan
lagg0: flags=8843<UP,BROADCAST,RUNNING,SIMPLEX,MULTICAST> metric 0 mtu 9000
options=1209b<RXCSUM,TXCSUM,VLAN_MTU,VLAN_HWTAGGING,VLAN_HWCSUM,WOL_MAGIC,VLAN_HWFILTER>
ether 00:90:7f:87:dc:78
inet6 fe80::290:7fff:fe87:dc79%lagg0 prefixlen 64 scopeid 0x12
nd6 options=21<PERFORMNUD,AUTO_LINKLOCAL>
media: Ethernet autoselect
status: no carrier
groups: lagg
laggproto lacp lagghash l2,l3,l4
laggport: em4 flags=0<>
laggport: em5 flags=0<>
lagg0.20: flags=8843<UP,BROADCAST,RUNNING,SIMPLEX,MULTICAST> metric 0 mtu 9000
options=3<RXCSUM,TXCSUM>
ether 00:90:7f:87:dc:78
inet6 fe80::290:7fff:fe87:dc79%lagg0.20 prefixlen 64 scopeid 0xc
nd6 options=21<PERFORMNUD,AUTO_LINKLOCAL>
media: Ethernet autoselect
status: no carrier
vlan: 20 vlanpcp: 0 parent interface: lagg0
groups: vlan