OK, so here is what happens when I try that.
1) Move auto.properties to other folder
2) Invoke freemind
3) Freemind 1.0.0 fires up right away with empty mindmap
4) Open 'old' mindmap #1 -- works OK
5) Open 'old' mindmap #2 -- also works OK
6) Close freemind without saving anything
7) Invoke freemind again
8) Click yes in dialogue box about opening mindmap from older version of freemind.
9) Wait forever...
Next I tried a variation on this. I edited out all references to last opened mindmap in auto.properties and left the abused file i place. Now freemind fires up in the same manner as if there was no auto.properties -- with the only difference that the Most Recent Files list is populated.
0.9.0 is not bothered by an auto.properties created by 1.0.0.