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A one handed weapon with the two handed trait is still a one handed weapon. This was covered in CRB clarifications.

Core Rulebook Clarifications wrote:

Pages 279–280 (Clarification): If I hold a weapon that requires 1 hand in 2 hands, is it a 2-handed weapon?

There are two answers to this.

For abilities that count the number of hands for a weapon while you're using it, such as an action with "Requirements You are wielding a one-handed melee weapon," count the actual number of hands you're using at the time. If you're holding a bastard sword in two hands, you couldn't use it with that ability. Weapons with the "1+" notation in their description, such as most bows, use both your hands when shooting, but leave you with a hand free for other actions the rest of the time.

Anything that's an intrinsic part of the weapon, such as a shifting rune, works differently. Reference the weapon's "Hands" entry in the weapons table—a bastard sword requires 1 hand, even though it gets a benefit in two hands from the two-hand trait. If you were holding a shifting bastard sword in two hands and activated it, you could turn it into a longsword (which you'd still be holding in two hands), but couldn't turn it into a greatsword (which requires 2 hands). For this purpose, "1" and "1+" are the same (though this doesn't matter for shifting since "1+" appears ranged weapons).

This was later added in PC1.

Player Core pg. 276 wrote:

If an action or other ability requires you to use a “two-handed weapon,” it applies for any weapon you wield in two hands. Any permanent adjustments to the weapon, such as a rune that can be added to a “one-handed weapon,” uses the Hands entry in the weapon table exactly (1+ counts as one-handed for this purpose).

In this case, The bastard sword is and will always be a one handed weapon for the purposes of being an implement or recieving runes. But it ceases to be a one-handed weapon for the purposes of fulfilling ability/action prerequisites of wielding such a weapon when...

Thank you for the clarification here, though I must ask, since thaumatuge requires only a one handed weapon, would it be wrong to house rule against the two handed trait counting? It's of course, only flavor, but it does specify "it leaves your other hand open to do magic runes or hold other esoterica"?

Quick question for you all, my friends last night figure out that thaumaturge might be able to use a two handed Bastard Sword as it's weapon implement, while i argued that since the two handed trait makes a weapon two handed, it's thus an invalid weapon for weapon implement, thus the bastard sword is no longer your implement. A clarification on this would be amazing if anyone has the time.