Dear Emily,
no, this is okay. For example if you want to extract the average beta/contrast estimates for a particular region, then the individual beta/contrast images are needed. There are several options for ROI analyses though, depends on what you want to obtain (a single p-value per contrast per ROI? extract the individual beta/contrast estimates for particular contrasts averaged for particular ROIs for analyses outside of SPM? getting percentage signal change values?).
Concerning the paths, basically you have two options. You can place the single-subject models or the corresponding beta/contrast images somewhere and rerun the Full factorial model - not elegant, but it works. Alternatively, go with spm_changepath('SPM.mat','C:\Data\','D:\Experiments\'); to replace the old paths. When using scripts there might also be the option to adjust the paths within the script with no adjustments on the SPM.mat required.
Hope this helps,
Helmut
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