We've had similar needs.  We typically create an API (and shared
secret) on the remote server that App Engine calls (or vice versa).
If you want to update the two systems independently you just need to
maintain backwards compatibility for a time.

For example, let's say AppEngine is your frontend and sometimes kicks
off a task to do the compilation.  You start a task with the "code to
be compiled" which then calls a JSON API (ex: www.my.com/api/compile/)
on the remote AWS server to start the compile.  The API could provide
a callback URL + unique ID for the AWS server to notify when the
compilation is complete.  When the compile is finished, the AWS server
sends the results + unique ID to the callback URL provided.

You could do all of it in AWS but as you've noted AppEngine has some
nice advantages.  The cost/benefit tradeoffs really come down to how
much of your system will be in AppEngine and how much in AWS.  It
sounds to me like AWS would just be a small backend piece for
processing and that all of the business-logic and data would live in
AppEngine.  That shouldn't be that hard to maintain if you keep the
systems logically separate with a well-defined API between them.

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