Which Pro version are you using when this is encountered and are there any additional details reported in the server manager logs or via Fiddler when the issue is encountered?
The error itself points to an issue with a recent geometry update, are any similar issues encountered with Validate?
@Anonymous User have you tried to upgrade ArcGIS Pro to a newer version?
I found the Enable/Disable Topology tool performing much better in ArcGIS Pro 2.7 comparing with ArcGIS Pro 2.5.1.
Thanks and good to know, Daniel. Our problem is we're locked into 2.5.1 for this client after experiencing larger issues in trying to upgrade Pro with the UN version we are at now. But we have heard that performance does improve with later versions, yes.