Hi Kamal,
Yes depending on your lan design it can affect STP topology change and may lead to STP convergance but only for those vlans which you are disallowing on the trunk.
For an example your root bridge connected to distribution switch which allows all vlans and for all vlans the path cost is already set for all access switches and now you disallowed some vlans from that trunk which will not even allow the bpdu for those vlans to pass through the trunk so now the bpdus for those vlans have to find new way to reach all downstream switches from root switch.
So I will always recommend you to have a full analysis of your network and then only plan for any changes and also arrange some downtime to observe the network behavior after changes.
HTH
Ankur
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