During checkpoint, WiredTiger writes out the checkpoint information into the table itself so that the table can be used alone as the input for session->create(..."import=(enabled,repair=true)") and the metadata for the create can be found in the file itself.

When a table's configuration setting is changed via session->alter, the metadata is updated, but the table itself is not marked dirty. This means that on the next checkpoint, the latest checkpoint information stored in the table itself will not reflect the successful alteration. If that table is then used for an import=(enabled,repair=true) then the newly imported table cannot find the correct altered configuration setting.