Pickysaurus

Have you looked in the Knowledge Base? https://modding.wiki/en/vortex/users/migrating-to-a-new-pc

It's not likely to be Vortex that is doing this. There was a fault with Engine Fixes that caused the game to disable all plugins, it's quite likely to be that. 

Check your extensions tab in Vortex. I am starting to suspect you have both the latest Starfield Extension AND an old version installed at the same time. This isn't possible unless one of them was manually installed at some point. 

Starting via Steam shouldn't make any difference. I am guessing you have SLocalSavePath in a SkyrimCustom.ini or something which overrides Skyrim.ini

Please see this article: https://help.nexusmods.com/article/105-i-have-reached-a-daily-or-hourly-limit-api-requests-have-been-consumed-rate-limit-exceeded-what-does-this-mean

If you installed the mods with Vortex originally, this article may help: https://modding.wiki/en/vortex/users/migrating-to-a-new-pc
 
If you install them manually or use any other tool, Vortex will not recognise them. 

This is answered in the thread below yours. Here's a link:
TL:DR - Wait for it to finish. It should only take a long time once. 

The user refers to the mod page pop-up that tells you you need at least Windows 10. They misunderstood that the "Download" button would proceed to download Vortex. 

Your account should be correct now. 

Changing it in the staging folder is the correct approach. 

Can you provide a screenshot of what's on the screen when it's frozen (if possible)? 
Something in your setup is likely to be causing the problem but at which specific point it freezes is quite important. I would suggest installing .NET 6 and the C++ Redistributables as this covers a lot of these problems. 

It's a server response, to it'd happen from any application making the same web request.
 
https://developer.mozilla.org/en-US/docs/Web/HTTP/Status/429
 
It sounds like you've used all of your API key requests for the given time period. If that is the case, you must've done an absolute tonne of downloading in a 24hr period.
 
https://help.nexusmods.com/article/105-i-have-reached-a-daily-or-hourly-limit-api-requests-have-been-consumed-rate-limit-exceeded-what-does-this-mean

Did you enable the plugins in the "Plugins" section of Vortex? 
That's the important part when it comes to saves. 

You can ask the current developer of the extension here: https://www.nexusmods.com/site/mods/110

This is covered in the pinned post: https://modding.wiki/en/vortex/users/dotnet
You need to install .NET 6

You may need to ask on the extension page as this isn't maintained by our team

Not sure if you know this, but SKSE has been available on Nexus Mods for a long time now. No need to drag and drop anything. https://www.nexusmods.com/skyrimspecialedition/mods/30379

Enabled states are stored in Vortex's internal state, you'd need to make an extension to access that information. 

You're not explaining your issue very well. It sounds like Vortex may have presented you with the "External changes" window and you chose not to accept the changes, which reverted the files to their last deployed state. This is intended behaviour. 

Delete archives are gone. You can redownload the mod from the website though. 

This is caused by an update to UE4SS - an update to Vortex will be available in the next few days. 

You're in a state where no game is actively managed. 
Head to "Games" and select the game there. 

Your E:\ drive also needs to have an NTFS file system. You should also specify which game you're playing - some games have to deploy to C:\ for some mods so unless everything is on C:\ you can't use all the deployment options. 

This isn't something that's possible to be caused by Vortex. It sounds like a hardware fault or worst case a virus/malware on your PC

There isn't a way to do what you're asking - that's part of the reason why Collections exist. Some of the mods you previously used may have been archived or deleted, which would prevent you from getting back to the same state anyway.