I was playing The Ark the other day and came across this quote from Truth’s hologram inside the Scarab: “I opened the Portal to this hallowed place, this shelter from Halo’s fire, in the hopes that more of our Covenant would follow us. Alas, save for a rabble of Heretics and their Demon allies, we are all that made the passage. Thus we must temper joy with sorrow in our hearts, for those who were left behind.”

Interesting. So other than Truth’s small fleet present after the Battle of Voi, apparently no other Covenant ships from Earth made it through the Portal (or if they did, they arrived too late).

I wondered how this is possible, as we know from the Data Drops that a number of Covenant ships remained in Arizona, and likely other places around the globe. They could have heard Truth’s call to follow him–though the Data Drops also mention the Covenant battlenet got scrambled following his departure–so my headcanon right now is that under orders from Hood, the UNSC Home Fleet, or what was left of it (minus the Forward Unto Dawn), set up a blockade around the Portal to prevent more Covenant ships from entering so as not to endanger the expedition task force that went through; Hood, as reluctant as he was, must have understood the importance of their safety despite not knowing the outcome on the other side and nor would he for at least another month.

I would think the protection of the Portal would be paramount, unless the “Flood army” he expected forced him to divert his fleet’s attention, at least until High Charity made a pass out of the Sol system the next day (re: Catalog interaction).

Has anyone else thought about this?

Pretty sure you hit the nail on the head. The ships that made it through were the ones there when the portal opened. The UNSC engaged what was left and a portion of the Arbiter’s fleet helped as well. I doubt it was so much as Hood understanding the importance as “Its the Covenant, we deal with them as usual”.
We know not ALL of them were dealt with either, the UNSC was dealing with cleanup operations for at least two years after the end of the war.