How to Fix ‘Apple Mail Messages Disappear from Inbox El Capitan’ Issue

OS X El Capitan is the twelfth release of OS X or macOS(as we know today). It was developed with security, performance, and stability in mind. It received reviews far better than the previous release Yosemite thanks to its superior features. However, there are a lot of major concerns for users when it comes to Mail app after upgrading the Mac system to El Capitan. Mail Issues such as freezing, crashing, emails missing and so on are experienced by users frequently. So today in this article, we are going to focus on one such issue which has made using Mail hell for users. ‘Apple Mail messages disappear from Inbox El Capitan’- an issue in which all or some Inbox emails suddenly goes missing. We will provide six different solutions to fix this issue. But first, let’s start by reviewing some queries to understand the problem:

“I just updated my MacBook to El Capitan. I know I should have backed up but I didn’t. Everything seems fine but I am missing hundreds of emails in Inbox. I saw similar queries regarding ‘Apple Mail missing emails El Capitan’ and still can’t seem to find a way to get them back. Please suggest some solution as those messages are pretty important to me. Thank you!”

“Everything was fine for a week after installing OS X El Capitan on my Macbook. But today when I opened Mail App to look for some bills from 2017, there are no emails in the Inbox. The other folders seem to be fine but my Inbox is totally empty. Since I keep all my messages in Inbox and never archive or delete them, I have no idea what happened and where they are. Some messages randomly show up if I search for them specifically, some not. I am so frustrated with this Apple Mail missing emails in El Capitan and would like a quick solution..!!”

Apple Mail Messages Disappear from Inbox El Capitan- What to do?

First and foremost, make sure you are actually looking for emails in the right account. It’s a basic thing to rule out before going for any other solution. Also, try using the first three solutions before moving on to rebuilding and reindexing the Inbox mailbox. Since they may take a considerable amount of time to finish depending on your Inbox data. Of course, you can avoid all this hassle by choosing the alternate option of using the MBOX Converter.

Now, to fix the Apple Mail Messages Disappear from Inbox El Capitan issue, use the methods mentioned below:

Preference Settings

Mail preferences can alter the viewing of emails of a particular mailbox or even an account. To make sure it’s not causing the Apple mail missing emails El Capitan issue, do the following:

1. Click Mail option >> Mail Preferences on the top blue ribbon
2. Now, click the Accounts tab
3. Re-enable the account by deselecting and then selecting the Enable this account checkbox
4. Also, select All messages and their attachments for offline viewing in the dropdown list.

Filter Settings

Message Filter if turned On filters specific emails and you seem to think the emails are missing. To turn it off, do as follows:

1. Open Mail app and click View option
2. Deselect the Enable Message Filter checkbox(if ON) to disable it.

Synchronization Issue

1. Choose Mailbox from the left side panel
2. Right-click to select Synchronize option
3. Now wait for the process to complete and check if it resolves the Apple Mail Messages Disappear from Inbox El Capitan Issue

Spotlight Indexing

Spotlight is responsible for search mechanism in Mail App. So at times, there are issues with Spotlight that results in the messages not being listed when searched. This makes users think that Apple Mail messages disappear from Inbox El Capitan after updating. To check it, follow the given instructions:

1. Go to Mac menu >> System Preferences
2. Open Spotlight and select Privacy tab
3. Use [-] button to remove the displayed folders
4. Save the settings and launch Mail to search for the missing emails again.

There is another way to force Spotlight to perform the reindexing process. To do that, follow the given steps:

1. Go to Applications >> Terminal >> Utilities Folder
2. Run the given command by pressing return key

mdimport -r/System/Library/Spotlight/Mail.mdimporter

Rebuild Inbox

Rebuilding the Inbox discards the existing messages and downloads them again from the mail server. It fixes most of the common issues in Mail App. However, it takes a lot of time depending on the size of your mailbox. To rebuild your Inbox, do the following:

Launch Apple Mail on your Macbook

Select Inbox mailbox

Go to Mailbox menu and click Rebuild.

Automated solution

It’s a disaster when Mail suddenly starts misbehaving, especially for professional users. And if you cannot even view your Inbox messages, then there’s no point in having a Mail client. There are manual methods of all sorts that users can try. But not a single one can guarantee the solution to ‘Apple Mail messages disappear from inbox El Capitan’ issue. Plus, rebuilding and reindexing takes a lot of time to process. So what to do? The solution is to opt for a third-party software. And what’s better than the Mac MBOX Converter to recover the Inbox mailbox in different formats. This tool is easy-to-use, quick and can convert all the Inbox items including the disappeared ones in one go. Its variety of relevant features makes it an effective choice for this task.

Final Words

Mail app is great when its running and working smoothly. But when it’s not, its a Mailing hell. El Capitan OS update was a major release for Apple Inc. It was loaded with new and improved features to enhance the user experience. But it also caused a lot of trouble for Apple Mail users. They kept experiencing different mail challenges after the update. In this article, we discussed one of those challenges(i.e., Apple Mail messages disappear from inbox El Capitan). Users can choose from the given manual solutions. Also, when everything fails we provided an expert automated tool to take care of your needs. Through the Mac Converter the Apple Mail missing emails El Capitan can be solved hassle-free.