If the SharePoint utility is run when the Enterprise Vault services are stopped, or the EV services stop during the SharePoint utility run, shortcuts will not get recalled.
The following error will be generated in the SharePoint utility logs.
Skipped. Vault unavailable or access denied. VaultUnavailable (-10005)
If seeing the error above in the SharePoint utility log, run the utility again with the recall option for the library which holds the skipped shortcut. Alternatively, if there are many libraries which have such shortcuts that failed to get recalled, run the archiving task again for that server or site collection, and then run the SharePoint utility again.
This issue has been addressed as part of the following release:
Enterprise Vault 9.0.3 - Release Details