If you have issues with the Platform Encryption Analyzer in Shield Extension, there are some troubleshooting tips that can sometimes help.
A Field Isn't Encrypted When Using the Platform Encryption Analyzer
Check for an email from Salesforce containing a reason for the failure.
From Salesforce Setup, in the Quick Find box, enter Encryption Policy, and then select Encrypt Fields. Check for additional information. If it's a standard field, try to encrypt the field from this page. For custom fields, navigate to the Object Manager and try to encrypt it from the field detail page.
Analysis Job Catches SOAP Fault Error on readReports in IDO and Client Org
Reports from the Salesforce Communities Management package are private, meaning Secure is currently unable to read them. This is due to a platform limitation and there is currently no permanent solution. This limitation can lead to fields being marked as “All Clear” for encryption when they should be marked “Blocked by Configuration”. This means a field could be encrypted, but there is a risk of breaking reports related to that field. The current workaround for this issue is to create a Batch Configuration, limiting the ReportFilterParserBatch to 1. This forces Secure to read the reports one by one instead of in batches.