If your connectivity across servers is good, then it should not break very often. To reinitialize, let's say it stopped working for 2 stores out of 50 stores. And let's say it stay broken for 2 hours. So now e.g. you have data upto 28thFeb, 9 AM and you fixed it at 11 AM. You miss 2 hrs data. This 2 hours data will need to be inserted using query manually. And to reinitialize,you may remove tables of those 2 stores from replication and add back with same settings. So if you add them at 11 AM, then data will start flowing from 11 AM onwards. The data older than 9 AM was all there. 9AM to 11 AM data you will need to insert with query.
If you don't want all data in single table, then you may replicate the databases individually, and then use joins to get data. Although it will be a big query if you have 100 databases. In my case, all data was always needed, so client asked for all data in single tables.