No, you should not use the self reset on loss of lock option in the ALTPLL megafunction when implementing PLL reconfiguration. The PLL may lose lock when PLL reconfiguration completes. If self-reset on loss of lock is enabled, the SCANDONE signal will be cleared. This may violate the minimum pulse width required to sample SCANDONE asserted at the ALTPLL_RECONFIG megafunction.
If the ALTPLL_RECONFIG megafunction does not detect SCANDONE asserted, the busy signal will remain high and no further reconfiguration operations will be possible until the ALTPLL_RECONFIG megafunction is reset by user logic.
The ALTPLL_RECONFIG megafunction will automatically reset the PLL when reconfiguration is complete.