Thanks for you reply Ian.
We are using a single datastore (ISCSI) for all VMDKs and 3 DELL host machines with Esxi 6.5 connected to single datastore. All these DELL Host machines are equipped with 120 GB RAM. There is no load balacing for this architecture.
Does VDP & Windows VM on same host machine can cause this issue? They are Windows VMs are of same type in another host machine connected to same data storage which is not effected during integrity checks.
I suggested I/O mainly because the VDP integrity check can be quite I/O intensive. If other VMs aren't affected, it may not be I/O contention.
Still, this sounds like some kind of resource contention issue. I'd recommend setting up monitoring for I/O utilization, memory, CPU, etc.. You should probably review the System and Application event logs on the Windows system to see if there is evidence of the root cause there.
VDP does not stop third party services on other guest VMs.