Two domain site: Link base URLs point to wrong domain

Try to install plugin duplicator and create a snapshot than with the install.php and related zipped file you need to copy in a subdir or in the root (copy all site an db in local for secure restoring) the two file and launch install.php, in a wizard there is a step in wich you can ridefine the path of your doman so you can recreate all your wordpress site on .com domain to stop flipping effect.
good luck!!!