Hi,
How much data is in your CI folder? When serializing your data Kentico stores a record in the DB which includes a hash specific to that environment. The restore tool uses that to quickly assess if it needs to update a record. Meaning locally it will quickly see what you've altered.
Likely you're target doesn't have those records or the hash mismatches, forcing the CI tool to check each and every single file as it might have changed.
Try limiting the amount of files you need or match the hashes.