After a week i transferred my beer into a secondary glass carboy, 5 gallon type and it is only about 3.5 gallons of beer. After boiling and transfering I lost alot. I measured the gravity during transfer at it was right where the finishing level should be, per the recipe.
Just to make sure I understand what your saying, did you take the brew out of the primary, then boil it, then put it into the secondary?
If this is the case, then you killed all the yeast and boiled the alcohol away. You only 'need' to boil the brew before you put it in the primary.
If I did read that wrong ... what was your initial gravity, and what is your final gravity?
If your gravity has dropped by at least half (ie 1.060 down to 1.030) and no amount of stirring and warming (just moving to a warmer room) gets the gravity down any, then you are fine to bottle. I've done this and ... knock on wood ... I haven't had any bottle bombs.