If your program is to run as a 32-bit application under Win 64 (as a WoW64 application) then you can be assured that everything will run fine if it runs under the corresponding 32-bit version of Windows.
If you are hoping to compile your program with a 64-bit version of Purebasic to run natively under Win 64 then there are no absolute guarantees that your code will run okay. There are certain things you have to change such as pointer variables being 64-bit and Win 64 does impose certain rules on structure alignments etc. However, my experience is that it is a relatively straight forward affair to get your code compiling and running under PB x64 / Win 64 and indeed to have a single source-base which is compatible with both PB x64 and PB x86.
I may look like a mule, but I'm not a complete ass.