You are right, typedef should work only in scope where it is defined, that is single file if it is at global level. The problem is how the files are combined when using BLITZ. Since typedef can't be "undone", it is impossible for BLITZ to solve such situation.
There are two simple solutions you can try (simple==not requiring to rewrite half of your program )
1) Use macros for the same effect: "typedef int _MyType_;" -> "#define _MyType_ int"
2) Switch BLITZ off for the files where you use this by adding "#pragma BLITZ_PROHIBIT"