Sync tables from Host1 to Host2 with over 50 million rows?
Master-Slave (and various other forms of replication) provide keeping two (or more) hosts in sync continually.  No ETL process needed.

Splitting the client processes and MySQL into separate servers is a good first step.

Putting different customers on different "shards" provides 'infinite' scalability in that dimension.  You would need some form of proxy or home-grown directing to get from a client to the necessary server.

Ingesting 60K rows is pretty trivial unless, of course, the data format is always something different.  At that point, I might contract a programmer who knows Perl (or other tool) to crank out ingestion scripts.  (Years ago, I did such with news feeds.)

Does 50M rows at 60K per customer mean you have 1000 customers?

I would suggest you use sharding do deal with excessive write traffic and disk space.  And use Slaves for excessive read traffic.

It is a never-ending pain to try to perfect "sync" scripts.