Currently, when a document contains an SPDX License ID marked as deprecated, it states "Invalid SPDX Document".

From the License List Documentation:

"When a license identifier is "deprecated" on the SPDX License List, it effectively means that there is an updated license identifier and the deprecated license identifier, while remaining valid, should no longer be used. "

If a document only contains validation messages due to deprecated license ID's, it should display a warning rather than invalid.