From: Cammeraygal Country
Expanding on what BBFB says:
1. If you use a scenario copied, and edited, in a saveable slot - above slot 25 - for a game, you can change scenario database items during a game started from that scenario.
2. You can change device specifications, and such edits will effect your in game devices. Beware, though, if you screw around with upgrade paths, you will get a flow on effect to TOEs, and end up FUBAR, unless you are right on top of what you are doing.
3. Broadly speaking, you can change aircraft type specs. Thus, you could change the Hellcat to fly at 420mph, or its replacement rate to some higher number (255 max). These will be taken up in the ongoing game.
4. Broadly speaking, you can change ship class specs. BBFB has said these will only be taken up on a future upgrade, but I do not 100% agree. Try changing the air capacity on an in-use carrier class and see what happens, as an example. However, BBFB is right in general terms. You can also create conversions for existing ship classes to other classes (including ones you create after the game started). It may be possible that you can change a device specification in a ship class armament slot - but not the number/turrets etc.
5. You can't change individual ships or airgroups (at least not directly, see point 3, conversions for an indirect route).
6. The Locations database contains ground units of all types, bases, and also TOEs. Most of this stuff you can't change once the game is running. But, you can, for example, as BBFB says, change daily arrival of supply/fuel at a base. Additionally, where a base already has some industry in a slot, you can change the amount of that ... but you can't add new industry items in new slots. You can also completely stuff up the TOES by making changes to device upgrade paths ... so don't do dat!
In my custom scenario, for the second edition, I have been working on a system where the US receive, from time to time, an AG clas ship, all named "Spare Hull II" at San Fransisco. These are a bare hull with conversion options to various CVL, CL, DD, PF (Tacoma) or a large LSM(R) assault ship, so the player has some flexibility as to what to do with them. Being a ~II name, you can change them to USS Sulaco, or as desired, the turn before arrival.
"You may find that having is not so nearly pleasing a thing as wanting. It is not logical, but it is often true."
- Cdr Spock