The free version of My Boy! emulator won't let me continue from my last save?

Question

I've been playing Pokemon Emerald for a couple of days using 'My Boy! Free - GBA Emulator' (found on the Google Play store).
I was saving a "quick" save in the emulator screen and also inside the game itself. Up until now it was working fine, but when I opened the emulator today and went into Pokemon Emerald, instead of having three options pop up on the screen which are "Continue", "New Game" and "Options" I only had the last two, without the "Continue" option.
I searched a bit through my storage and found the save files for the game, but the game simply doesn't recognize them for some reason. It worked fine until today.
The ROM is inside a zip folder which is inside Downloads (I've set the My Boy app to find games there), and the save file is inside a folder called "saves" which is inside the "MyBoy" folder.

Updates:
I tried putting them in the same directory (the game is stored on the device's internal storage) and it still won't work. (It is the same save file that I was used before it stopped working) Is there anything else I could do? –
I've also just noticed that even though the game is stored on the device's internal storage the save file is in storage/emulated/0/MyBoy/save/ and the game is in storage/emulated/0/Download/
Any clues on what I can do?

Robotnik · Answer

Comments originally posted under the question converted into a wiki answer. Credit: Mr. Mendelli:

I did some extensive testing, and have made some discoveries.

First, ensure that the ROM name and save names match (excluding their file extensions). So for example:

Gamename.gba
Gamename.sav

If the game is stored on the device's internal storage, the save file must be in the same directory as the ROM. If the game is stored externally, i.e. an SD card or USB drive, the save file will be written to the following location:

storage/emulated/0/MyBoy/save/

This means that if your game is in storage/emulated/0/Download/, then the save file will be somewhere in that folder. If it is not, than you have either lost it, it's name does not match, or it has been deleted.

I place my games on my microSD card in: /Games/GameBoy Advance/. I have noticed that in most (not all) similar cases, the user has misplaced or accidentally deleted their save due to disorganization or storage clutter. I always advise keeping any devices storage as neat as possible to avoid misplaced data and files.

The free version of My Boy! emulator won't let me continue from my last save?

Updates:

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