ixgbe: fix timestamp configuration code

The commit in fixes introduced flags to control the status of hardware
configuration while processing packets. At the same time another structure
is used to provide configuration of timestamper to user-space applications.
The way it was coded makes this structures go out of sync easily. The
repro is easy for 82599 chips:

[root@hostname ~]# hwstamp_ctl -i eth0 -r 12 -t 1
current settings:
tx_type 0
rx_filter 0
new settings:
tx_type 1
rx_filter 12

The eth0 device is properly configured to timestamp any PTPv2 events.

[root@hostname ~]# hwstamp_ctl -i eth0 -r 1 -t 1
current settings:
tx_type 1
rx_filter 12
SIOCSHWTSTAMP failed: Numerical result out of range
The requested time stamping mode is not supported by the hardware.

The error is properly returned because HW doesn't support all packets
timestamping. But the adapter->flags is cleared of timestamp flags
even though no HW configuration was done. From that point no RX timestamps
are received by user-space application. But configuration shows good
values:

[root@hostname ~]# hwstamp_ctl -i eth0
current settings:
tx_type 1
rx_filter 12

Fix the issue by applying new flags only when the HW was actually
configured.

Fixes: a9763f3c

 ("ixgbe: Update PTP to support X550EM_x devices")
Signed-off-by: Vadim Fedorenko <vadim.fedorenko@linux.dev>
Reviewed-by: Simon Horman <horms@kernel.org>
Tested-by: Pucha Himasekhar Reddy <himasekharx.reddy.pucha@intel.com> (A Contingent worker at Intel)
Signed-off-by: Tony Nguyen <anthony.l.nguyen@intel.com>
Signed-off-by: David S. Miller <davem@davemloft.net>