Loss of Breakpoint Ability

I've a recurrent problem. My breakpoints stop working (i.e. they get ignored). This seems to be correlated with how I move my code around. Specifically I work on a desktop and sometimes on a workspace off a usb on a laptop.  To move code I copy the src folder over.  I've been able to establish situations where on my USB workspace the breakpoint still works (on same code) even though that same breakpoint does not work on the same code on the desktop.
  I think I was able to fix it once by rebuilding on the desktop the whole project (i.e. manually creating an new folder, copying code over etc).
Any idea what I might be doing by my process of moving src folder that gradually seems to destroy my breakpointing ability? I'm thinking some cache or index or other workspace specific context must be causing the issue.
  I did try copying my full USB workspace over (where the breakpoint works) to desktop. But didn't resolve.
  So two questions:
1) how might i fix the problem (otherwise debuggin becomes very hard)
2) is there some better way for me to move code between workspaces? Perhaps some kind of source control process or syncing process within eclipse?
  Thanks!
   Lin