Well: when replicator runs, it takes a kind of "snapshot" of things to do and works on them. That said, it will not be a problem, to run both tasks simultaneously, but might cause some disk io peaks.
I would recommend to schedule replication after the agent run, to not have to much performance impact on the server.
And I would check,if it really is necessary to change ALL documents in that database on every agent run, as usually this is just because of some lazyness of programmers and not very often really is necessary...