Did you notice any significant change?
If possible, would you mind trying out our 4.5 Beta? We’ve made some changes to verification algorithms and that may impact the sync speed. The information about 4.5 Beta2 and links are available here: MainWP 4.5 BETA [RELEASED] - #2 by bogdan
The size of action logs table shouldn’t affect the sync speed but it is also completely safe to delete the table. And if you are not actively relying on Action Logs, you can even disable it.
Navigate to Dashboard > Info > Action Logs page, and click the Delete Log button to delete the table. To disable it, select Disabled from the dropdown and click Save Settings.
Finally, if neither of those help, can you try temporarily deactivating non-MainWP plugins and see how that affects the sync speed? Some plugins like WF and UDP are known to be heavy on resources.