Heya!
Yes, it should be possible. AFAIK, user-placed markers will be named something akin to "USER_DEFINED_#" (with # being based on number of markers already in mission); at least they were in OFP (check out this script:
clickety by snYpir). However it's always possible the naming convention will have changed in Arma 2, in which case we're in a bit of a pickle.
Anyway, if you CAN collect the user markers using for instance the script above, it's simple a matter of collecting the info on the marker's pos and saving them in a global var and then loading them in the next mission
Apparently snYpir's script goes ga-ga if you delete markers though, which I can totally understand.
An easier method, incredibly enough, might actually be to use a onMapSingleClick-based script to create your own markers, which removes the need to collect data about user-made markers. Then you'll have all the info you need already. You could for instance have a radio command, "Report in target positions", which would begin the script (adding an action/radio command "Finish report"). While the script is running it'd monitor onmapsingleclicks, and add those to the target arrays. Handling mis-clicks could be done e.g. through the radio screen as well (remove latest etc.). It'd be a pretty complex script, but I think players of your mission would really appreciate it! And if you get it done, feel free to post it here as well
Wolfrug out.