from
https://electrum.readthedocs.io/en/latest/faq.html:
Note that the address will be shown with a red background in the address tab to indicate that it is beyond the gap limit. The red color will remain until the gap is filled.
Basically, increasing your gap limit untill no red addresses remain should do the trick...
Since a gap limit of 50 seems to be insufficient, try:
wallet.change_gap_limit(500)
wallet.storage.write()
if that isn't enough, increase the gap limit untill no more red addresses remain...
But am i right in my newfound assumption that you created a wallet with 60.000 addresses, then randomly picked an address each time you wanted to receive a payment instead of using incremental addresses? If so, odds are that your problem isn't easily solvable because electrum wasn't coded for this usecase.... See the link posted by RapTarX.
If you followed best practices and used incremental receiving addresses, there should be no problem (AFAIK), but if you picked random addresses, electrum will stop deriving new addresses as soon as it derived x unused addresses (x = gap limit). By picking random addresses, the derivation will stop as soon as you left a gap between 2 used addresses that's bigger than the gap limit.
In this (nonstandard) case, i guess it would be best to create a new wallet and send all funds from your wallet with 60.000 private keys (and public keys, and addresses) to the new wallet... But this time, don't pre-generate 60k addresses, just use the gui to show you a new receiving address each time you want to receive a payment... The gui will usually show you the first unused address it derived instead of picking a random one, so by following these best practices, you won't end up with a huge wallet full of gaps in the future...
A different approach would be to export the private keys of the funded addresses and import them into a different wallet (right click on every address with a nonzero balance and chose "private key", save them in an ascii file, import them into a new wallet... (warning: if you pc is compromised in any way, this is a very dangerous process)...
Just make sure you always hold on to the 60k wallet, since you never know if somebody is ever going to fund one of your old addresses (either by mistake, or as a habit).