Let's answer these two questions

[Cesrate]

http://wiki.kerbalspaceprogram.com/wiki/Extend-o-matic_Series_A1_Deployable_Flag

* Can a Kerbal recover more than one flag and later plant multiple?

* What happens to the selected flag when to crafts dock together?

[J0hnsmine]

1. yes2.--- er--- i thiiiin k the craft you do To.

[regex]

Pretty sure when the Kerbal enters a pod any extra flags are replaced by their single replacement flag. At least, that's what I remember happening.

[CosmicScientist]

First one, yes but I last remember not having additional flags to plant after recovery, if you re-enter a command pod, you gain that vessel's flag type to plant depending as to what you set the flag to, so in essence, you can plant infinite flags as you can use infinite mono propellant with a Kerbal's jetpack.

Second one, try it, you really don't need much to just dock two rovers together at the KSC to find out. My guess it's the one you're selecting when it's docking that overwrites the other and I have no clue about what happens if you undock.

Oh and just in-case this is interesting to you, the date of all flags planted will be shown in the tracking station.