I just did that and yes, the scheduler get replaced and worse, all schedule jobs stops working too!
Now the scheduler only works for the R2 site, not for the 4.x and 5 R1 sites :(
A fix for this ASAP would be nice!
Try following in your R1 webconfig.worked for me
<assemblyIdentity name="EPiServer.Scheduler.WKTL" publicKeyToken="8fe83dea738b45b7" culture="neutral" />
<bindingRedirect oldVersion="126.96.36.199-5.65535.65535.65535" newVersion="5.1.422.4" />
Can anyone confirm that this fix works, and that R2 can be installed on the same server as an R1 site is running?