There are two rules that may help here...
First, The Watcom Rule states "Watcom Does Things The Way They Should Be Done".
If The Watcom Rule applies here then the answer is "yes, you can execute multiple separate consecutive pairs of START / STOP SYNCHRONIZATION SCHEMA CHANGE" statements.
Second, The MobiLink Rule states "You must test ever single synchronization setup change before implementing it."
One way to do this is to use your local MobiLink test setup that consists of a test consolidated database and two or more test remote databases. You do have a local test setup, right? Of course you do ;]
Testing will determine whether two START / STOP pairs will work; the Watcom Rule tells you it's worthwhile testing.