In the time you have waited for someoen to respond to this post, you could have done half of them by hand... Anyway, a simple method would be to import them as a sequence in a pre-comp and use time-remapping on that pre-comp in the main comp, then animate the value over time. Simply make the comp long enough and render all flags. You can always split up the resulting clip/ image sequence later if needed.
In your first comp select all changed properties in your flag by selecting the layer in the timeline and press the U key twice. I'm assuming from your description that there is only one layer in the comp.
Now loop select all of these properties and go to Animation>Save Animation Preset and save the preset.
Now select the other 199 flags from your Project Panel and drag them into the new composition icon or Context click, or go to File and select New Comp from selection. When the window pops up select Multiple compositions and then click OK.
Open the compositions, select the footage layer and press Ctre/Alt+Cmnd/Ctrl+Shift+F to apply the animation preset you just saved (or used).
Repeat for each new comp
Set up a new output module preset for the render settings you want to use and set that one as the default or pick a render setting in the AME you want to use and set that as the default for a watch folder.
Then, select all 200 comps in the timeline and choose Composition, Add to Render Cue and press Render OR
Save your AE project to the Watch folder and let the AME do it's thing.
You'd be done by now...
This whole operation could be written as a script but it would take less time to just do it with an animation preset.