You do not tell the linker that you use the memory at 0x6000. So the SREC file does not contain any values for that memory - when you load the new application, this part of memory stays the same.
If you don't initialize memory with a specific value, you should treat it as undefined (= garbage). Adding one to an undefined value is still undefined, just one larger.
About the read/write thing: Both Epiphany and the host can change the values at any time, but the compiler does not know that. Mark the variable on the Epiphany as "volatile" and think about the timing (especially the order of doing things, avoid "at the same time" unless you know what you're doing).