Hi Parasto,
there are multiple places in TopBraid products where SHACL
validation results are displayed. Are you referring to TBC or EDG?
In EDG, is this about the Data Validity over time chart on the
Dashboard panel, or the Problems and Suggestions panel? (In both
cases I don't think we have ways to clear them but if you could
clarify your requirements I can record a feature request for you).
Holger
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Ok, so you have used the Refresh and Show Problems button from
the tool bar 
This Problems metadata is stored in Eclipse and would only disappear if you delete or rename the file that caused the Problems. However, see
you can right-click on the items and Delete them if needed.
For SHACL, I would simply use the SHACL Validation view as its content is not persisted between sessions, and also provides more info and better ways of navigating to resources:

Use Window > Show View > SHACL Validation if this panel
isn't visible.
HTH
Holger
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