To answer your question, yes technically the date is stored in zulu format but what you see in the interface is a pretty format. However my apologies but I don't understand how the modified comes into your 3 day reminder. What exactly is your criteria for sending reminders? 3 days from created or modified or some other arbitrary date? If so, again I would suggest doing it differently.
Your goal is to send a reminder only at the right specific day which for discussion purposes say its 3 days past the last modified date. One way is to create a calculated column in the library called Reminder Date and have that formula be like =[modified]+3, and format the output as date. Then have your Flow run daily, get all items where today = Reminder Date (as I showed above). Then send reminder email.
Or you could bypass the Reminder Date in SharePoint and just do the 3 day calculation in an expression in Flow. On the filter of the get files, you would say adddays(modified, 3) eq today. That isnt exact but you get my meaning.
You don't need the flow to fire on created or modified if your only goal is to send a reminder of files for files that are due on a certain day. If you want to discuss more, please go into more detail of your requirements so I can better recommend a solution. Thanks!
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