First reset the Windows Time Service configuration and clear the condition that is causing W32Time to remain in a spike state. On the affected DC, run an elevated Command Prompt and execute: w32tm /config /update /manualpeerlist:"" /syncfromflags:DOMHIER. Then restart the service with net stop w32time followed by net start w32time.
Next, force the controller to rediscover the domain time hierarchy and synchronize: w32tm /resync /rediscover. If it reports that the computer did not resync because no time data was available, check w32tm /query /source and w32tm /query /status to verify that the DC is using the expected domain time source. On a domain controller, you generally want the PDC Emulator to obtain time from a reliable external source, while the other DCs synchronize through the domain hierarchy.
If the large offset is causing W32Time to reject the correction, you can temporarily increase the allowed phase offset rather than permanently changing the domain's normal time behavior. The relevant registry value is MaxAllowedPhaseOffset under HKLM\SYSTEM\CurrentControlSet\Services\W32Time\Config - it is measured in seconds. After changing it, restart W32Time and run w32tm /resync /rediscover. Once synchronization succeeds, return the value to your normal policy/configuration rather than leaving an excessively large threshold in place.
For virtualized DCs check the hypervisor's time synchronization integration. The domain time hierarchy should be authoritative for the guest, and you should avoid having both the hypervisor integration service and W32Time independently correcting the DC's clock. For a PDC Emulator in particular, establish a reliable external NTP source and let the remaining domain controllers and domain members follow the AD time hierarchy. Finally, verify the result with w32tm /query /status and w32tm /query /source - repeatedly large offsets usually indicate an underlying VM pause/resume, hypervisor time-sync, host clock, or virtualization configuration problem rather than simply a W32Time threshold issue.
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hth
Marcin