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The True Sith Empire has reemerged with updated weapons and invades the GA. Standing in their way is the current Jedi Order and the GA military. Can the GA and Jedi emerge the victor or do they fall?

"Updated weapons" is a little vague. Assuming their war materiel is on par with the GA, then the Sith stomp. The GA is in tatters after three successive wars and there's only a couple hundred Jedi Knights.

We need more vagueness in this thread. Add some jawas in Star Destroyers.

A lot would depend on alliances GA makes. They would need to unite with confederacy(Corellia, Botawue and some other worlds). Hapan sector is likely will be on their side as their queen is Jedi. If they persuade Chiss to help them, then victory is guarantied.
Also, this Empire would need at least have some superior technologies. For example, Yuzhan Vong had technologies that Republic simply couldn't counter, they caused much greater damage to republic and ultimately made it fall apart, while Sith Empire established only partial control of the galaxy. Yet, newly formed GA still managed to defeat Yuzhan Vong.


The GA is in tatters after three successive wars and there's only a couple hundred Jedi Knights.

While they are in tatters, those wars taught them harsh lesson. The galaxy is in most military based state as it ever was. It takes them much quicker to mobilize army and they generally dedicate more resources on military, than Old Republic. Yes, there are far less Jedi but it is quality, not quantity that grands victory. In Apocalypse thousands Sith invaded Coruscant including Abeloth herself, yet, Jedi defeated them and drove survivors back.

Vitiate has proven himself to be a strategist par excellence {in the realm of long term politics, anyways} and given tensions between the GA & the former Confederacy, it's entirely possible that he may be able to persuade them and the Remnant to join him.

As far as Apocalypse is concerned, I confess to not having read it entirely. The Jedi really repulsed thousands of Sith warriors?

Vitiate has proven himself to be a strategist par excellence {in the realm of long term politics, anyways} and given tensions between the GA & the former Confederacy, it's entirely possible that he may be able to persuade them and the Remnant to join him.
I quite agree with that. For Remnant to join he would need to assassinate Jagged but he left position at the end of the last novel anyway. Not sure about confederacy, though, as Jacen's actions made them unite with GA and particularly fear Sith.

Obviously it wasn't open field like on some pictures . Also, majority of those Sith were weak in the Force, a lot of them couldn't even deflect blaster bolts, if shooter was aiming precisely in different points.
Another thing is that Jedi were more versatile. For instance, they could hide in the Force. Utilize battle meld, which disappointingly wasn't represented in the book.

At first Jedi were taking Sith out in Splinter Cell style. Then all Sith relocated to Jedi Temple and barricaded in there. Don't remember exact number but it was over 2000. Jedi had advantage as it was their territory. They got help from military volunteers with blast bots, however, they couldn't help, until Jedi disabled temple shielding. So a few selected Jedi penetrated temple, while majority were waiting outside. Shortly speaking Jaina, Luke and Corran were stomping. "Typically" against all odds they managed to disable shields and then rest of Jedi and soldiers got into action, which was described only vaguely. Also, soldiers were prepared with tools and weapons effective against Sith. For example, Saba and Tahiri with organised unit of soldiers killed plenty of Sith on their way with use of clever tactics and positioning right to the point of reaching one of the Abeloths and Saba biting her head off.

In short, the Jedi of the NJO are mostly badasses who had war experience and worked with the army, while a lot of the Sith were mooks.