If each player can't immediately agree on how many cards Alice tucked to the bottom of her library with Thassa, then we could help them remember by asking Alice if she remembers the first card that she put on the bottom of her library. If she does, then whatever cards are underneath that card near the bottom of the library were also put there with scry.

After Alice tells me the name of the card away from the table, we can lift her deck and look at all those bottom cards underneath the first card she scryed to the bottom with Thassa. Count those cards starting from the 1st card scryed and ask each player “Based on the answer Alice has given me, it would suggest that ‘#’ cards were sent to the bottom of the library. Can you each recall if that was the exact number of cards you remember were put on the bottom of this deck?” Maybe both Alice and her opponent will remember now and agree on the number. Sometimes asking questions that get players to start thinking about things can suddenly stir up their memory and help them remember things that happened.

The drawback to this fix is if the first card Alice scryed to the bottom was a land card or any other card that she has multiple copies of in her deck because she could have scryed more than one of those same cards away.

My answer is similar to that of Glenn Fisher's post above, except I would confirm the number of cards with her opponent before randomizing the deck in order to eliminate any advantage she could gain from having scryed cards get mixed into the deck.

Greetings judges! Thank you for a great week of discussion on this topic.
And as Fergie taught us, Big Girls Don't Cry, and there really isn't any
reason that Alice will need to cry over her Scrys.

The MIPG tells us that Alice has committed Looking at Extra Cards. She has
seen an extra card that she should not know the identity of, but has not
drawn the extra card. The Additional Remedy section tells us that we need
to shuffle the randomized portion of the deck. This means that as a judge,
we must survey the field to determine if there are any cards that could
have manipulated the deck in some way and ask the players the same. In this
game we have a Thassa that has been in play for multiple turns. This far
into the game, it is also likely that the players will not know exactly how
many times Alice has put a card on the bottom of her library with Thassa.
We can ask the players and try to get a consensus on how many cards were
put on the bottom. While we want to get to the right number, it doesn't
have to be exactly right. If X cards were put on bottom, that leaves N
random cards above them. If we happen to leave X+1 and shuffle N-1, the end
result will still be N random cards above the X Scryed cards. Also, kudos
to Eric Paré for the suggestion of asking Alice away from the table if she
remembers the first card put on the bottom. You should also ask if they put
more than one copy on the bottom to make sure we're going to the right spot
if you can use this method.

Set the top card aside since this is the card that Alice was supposed to be
able to see and set aside the number of cards from the bottom that you and
the players have agreed on. With the remaining deck, shuffle the deck then
place the cards set aside in their appropriate positions on the top and
bottom of the deck. Alice can then proceed with her Scry and continue the
game. Alice receives a Warning for Looking at Extra Cards.