The problem is that “Changed by Another Program” setting is already set to Prompt for all my configurations, and the file I’m opening is definitely less than 300 MB – it’s just a usual small Perl file (23 Kbytes in size, actually).
And, besides, if it were one of the options you just mentioned, the file would be locked all the time it is opened in EmEditor (or did I misunderstand something?), while in my situation it is locked for very short period of time – only when it is being opened by EE, and after it is loaded into EE, the file becomes fully accessible again, even though it is shown in EE window. So, it must be not the lock you were talking about, it’s something else…