I know that some mods, when added, need you to be in a secluded space and ask you wait for cells to respawn (default 3 days). So my question is:

I have my cell respawn to 6 months (yeah, I know, too long, but it helps with my idea of realism). If I add a mod that needs the cells to reset, my only real option is to set cell respawn to 3 days or less and wait that long for the cell respawn. However, I will lose the emptiness I wanted by having a 6 month respawn,. All the plants will be respawned, new aenemies in the places I creared, etc. So, is there a better solutio or am I SOL?

It depends on what the mod does. Does it affect the whole world or only a few special cells? The respawn time setting is checked whenever a cell is loaded, but not before. That means if your respawn time is set to 3 days and you wait in the IC shack for 3 days, then save and set the respawn time back to 6 months before leaving the shack exactly nothing will happen. The world will still be as empty as before and nothing new will spawn since the game will look at your respawn time only when a new cell is loaded. So knowing which mod you have in mind would help.

Thanks for the info Phitt. No specific mod in particular, just doing some tweaking on my 5 hour game and am having an AN issue which I think I need to reinstall and this came to mind (although it may not apply to weather mods). So figure I ask ahead of time as I will also look at adding some other mods later today (and yeas, looking at their manual).