@Federico_Ciuffardi - Got it 
Since you won’t be able to use the Atlas Admin API to resume the free tier clusters (as Chris and Kushagra have mentioned), you could try automating / scheduling a connection to the M0 cluster’s you have running before the 60 days of inactivity to prevent it from being paused in the first place as a workaround possibly… I haven’t tested this myself but seems like it might work for your use case?
Let me know your thoughts.