Is it okay to query the same agents who rejected you if you make significant changes to the novel (though the title is the same)? If so, should I mention that I've queried them before but that now the novel has been restructured?
In more detail, I queried with a science fiction novel that was 195,000 words and got form rejections. I've since edited it and restructured it to 125,000 and am unsure how to go about sending queries to the same agents with the assumption that the word count was what led to the rejections.
You should start with the agents you haven't queried before.
While I think you're right to guess that word count was an instant pass, you don't know for sure.
If you do requery, mention this is a slimmed down version of an earlier query. You don't need to use "that you passed on" in this query, cause if you're querying now I can figure that out.
What you haven't realized yet though is if the ONLY problem was word count, a savvy agent would likely have said that. "This is a terrific concept, and good if wordy first pages but you need to chop 50K" kind of thing. Of course, some less-savvy agents (ahem) might reject without actually looking at the writing or thinking about the plot. I've requested and READ novels of 150K in the past. But I've also sent a lot of writers packing when they told me the word count was 200K+.
Most recently I ran into a nice fellow at #WDC18 who had north of 200K, and would not be persuaded it was too much, because "an editor" told him the novel was great. I did ask if the editor accompanied that assessment with an offer of publication (no, she did not) but I don't think he got that message.
Back to you though: Before you query, make sure your query is polished up. The QueryShark archives will help you avoid some very common stumbling blocks.