Neither is adequately documented, so answering the questions is dicey for all except those who have the VFP source code available to them. So here is offered my OPINIONS for the answers to your questions:
>I have a couple of questions:
>
>What is the difference between FLUSH and SYS(1104), and when should you do one or the other?

Sys(1104) seems to do extra memory purging/freeing, on a wide basis. FLUSH may not even actually free memory so much as purge certain content to media.
I would tend to use FLUSH in the general case and SYS(1104) as when a sledgehammer seems called for.
BE ADVISED: in more recent Windows systems, FLUSH only 'tells' the OS that certain file buffers need flushing andrelies on the OS to actually (get around to) do it.
>
>Second, is the FLUSH command for all information in all tables, or do I have to do a FLUSH for each table?

FLUSH is for all FLUSHable data buffers and it is unclear if this can include records still under lock by the flush-issuing system. My guess is that it does flush them too.
FLUSH will NOT (we have guessed) touch buffered (row or table) records that have not been TABLEUPDATE()d, explicitly or implied.
FLUSH will NOT touch records under TRANSACTION control.