MySQL replication - slave update
Answers to your questions are as below: 

1) Will it mess up the sync in any way

Answer: Yes it will mess up your replication process as slave reads from relay log and updates on Server.
For example: If a row has been added to slave and which is not there in Master then "INSERT INTO ..." query will fail which can cause replication process being stopped.

2) Will the changes get overwritten from the master during the next replication event, Can I make above (2) option happen ? 

Answer: NO. but there is a alternative you can use pt-table-sync tool

This tool changes data, so for maximum safety, you should back up your data before using it. When synchronizing a server that is a replication slave with the --replicate or --sync-to-master methods, it always makes the changes on the replication master, never the replication slave directly. This is in general the only safe way to bring a replica back in sync with its master; 

Note: It is a good idea to set slaves as read_only 
This variable may help prevent some unsafe writes from occurring on slaves, but only if users are not needlessly granted the SUPER privilege.