Combining Sub-Samples for Factor Analysis?

I am a newbie on the site and a relative newbie to some of the analysis I am trying, so my apologies in advance for any rookie mistakes or for asking what might be obvious to others!

Can I run a single factor analysis if the data is from multiple sub-samples? By this, I mean that some subjects respond to the same items in one situation and others respond to the same items in another situation. For example, suppose that I am looking at the construct of room comfort by measuring temperature, humidity and lighting, and I measure these 3 items from 50 subjects in a cold room, and then I measure these 3 items from 50 different subjects in a hot room. Is it defensible to run a single factor analysis with 100 observations for each of the 3 items (50 observations from hot room subjects and 50 from cold room subjects)? Or can we only do factor analysis if the same subjects provide responses in a cold room and in a hot room (still 100 observations but the same sub-sample providing repeated responses).

I looked on the site and found some answers about missing data (not all subjects respond to all items), but nothing about what I am looking at, so I would be grateful for any inputs.

Thanks for any guidance!