What you did in the end was more or less the same as creating a new wallet and moving all funds to this new wallet... The big difference is that you sweeped all funds into the first couple of addresses of your existing wallet instead of creating an actual new wallet (by using the same seed as the previous wallet, you restored your old wallet instead of creating a new one).

All in all, this shouldn't be a real problem... As soon as you start deriving addresses that have a history, you'll see some extra transaction history, but that should be about it.

The thing is still wanted to stress (i'm repeating myself here): i don't think there is a real life situation where you'd actually need to pre-generate 60.000, 40.000 or even 5.000 addresses. Nor is there a situation any situation where you'd ever need to leave a gap between 2 derived addresses. It's best just to create a wallet, leave the gap limit at 20 and just use the next unused address in the list (or use the receive-tab, which will automatically present you with the next available, unused address).
There is no real benefit in leaving gaps, other than some security trough obscurity.

But i'm happy you got your problem sorted out. There's no real like-button on bitcointalk, but the post in which you gave thanks to the posters in this thread is certainly appreciated
By the way, it would be nice if you could lock this topic. If you keep a topic open after the problem has been resolved, spammers will keep on replying to this topic in the future.

It is not visible by default. Only you see it when looking at your own profile, but not others.

In any case, go to your profile, then to account related settings, and check that “Hide email address from public?” is ticked.