In this case i thought the 'extra' 5% was just lost....no? I'm pretty sure if you repair a 60% with a 60% you'll get 100% and lose 20% but I may be wrong.
There may be a certain amount of loss but it's not a complete one the way you're suggesting. I'm not really sure what the mechanics are. I was just using that as an example more than anything. But you can't simply use an inferior weapon to repair any other weapon. If the two combined come out to more than 100%, then you can't repair either one.
PS: Aaah so your Repair skill also factors in. This is from the Portal:
The final condition of the item being repaired is equal to (condition of the less damaged item) + 5%*(condition of the more damaged item) + 5% + 0.15%*(player's repair skill level). For example, combining a 20% minigun and a 10% minigun by a player with 10 points in repair skill will result in 20%+0.5%+5%+1.5%=27% final condition. The same repair performed by a player with 50 points in repair, will give a 33% condition minigun. Other than determining the item type, it doesn't matter if you repair item A with item B or the other way around. (The formula also works when the two items have different item HP even if one of them is unique — the item conditions are taken into account, not HP.)
So even if you have one gun at 60% and another 40%, you can't repair them since your Repair skill will put the total over 100%.