"VFP 9.0 does not share a common filing system with 5.0 "
By that I assume that you mean "Does not share a common data table/database directory".
Since, as Mike says above, VFP9 can readily utilize the VFP5 data tables/databases with NO "conversion", why not just make the VFP9 application share the tables?
"My database is on VFP 5.0 on windows 98 and I wish to transfer same database to run on VFP 9.0 on windows XP"
Unless, for some unique reason, you want this VFP9 application to be TOTALLY resident on a single workstation, you will NOT want your data tables/databases on the workstation (and within its workstation OS) at all.
Instead you will want the data tables/databases on a Server in your network where both the VFP9 and VFP5 applications can share the files. (Obviously your VFP5 & VFP9 code would need to be modified to access the data tables from the Server.)
Good Luck,
JRB-Bldr