Some emails are there when searching, but do not show up in inbox for mail account. How do we permanently fix that? This is dangerous for businesses that rely

Hi, and thanks,
I noticed that many dozens of others have expressed the same problem with Thunderbird, but it still continues.
For no apparent reason, sporadically, some emails don't show up in the inbox list of an account, but are actually there. If we're told later that someone sent one, and if we do a search at that time, it does come up!
We rely on this for business, and wouldn't know to search if we are unaware that an email has come in but simply doesn't appear in the list. We have actually lost significant business $ on 3 separate occasions, from clients who have said they emailed us, but we never responded! (That's really bad, and even worse because they also won't use us any more.)
Obviously, we of course would not want to have to check with the webmail host when we have Thunderbird. So...., how can we permanently fix this problem so it never, ever occurs??? We used to use Eudora before switching, and this never happened.
Some blogs say to delete one of the files in the system to re-index the inboxes, but again, that would not be the answer, because we wouldn't know to do that, nor when to do that, since some emails, without a warning or clue, occasionally simply don't show up in the list at all.
Please let us know the permanent and complete fix for this ASAP.
Thanks so much,
Les Pock

Lers, I have used Thunderbird for the best part of a decade and have only once experienced something similar to what you describe and it was a corrupt database.
So lets just back up a bit.
If you want mail to flow without issue the first bullet to bite is anti virus.
* Scanning of outgoing mail is a total waste of time and an added risk for no return. You anti virus already certifies your machine clean.
* Scanning of incoming mail is of extremely limited value. Thunderbird does not allow scripts in email, so there is no bug that will junmp out and start running even if your mail is not scanned and it contains a virus. The exception to that is attachments. But they are not dangerous either, unless you try and open them. Even then your anti virus should be monitoring the temporary folder on your computer and blocking any attempt to write the infected file, let alone execute the contents.
* Scanning of your mail folder likewise is of limited value, but is more than often the cause of mail indexes not being updated. These days anti virus program appear to scan everything. Every file as it is accessed and opened. Thunderbird often has quite large files to store mail, up to 4Gb is not all that uncommon. Anti virus program take about 2 minuted per Gigabyte to scan files. So it can be the case that the anti virus is scanning while Thunderbird is timing out waiting for access to the appropriate files.
To make things more efficient exclude your Thunderbird mail profile folders from on access scanning by your anti virus program. The folders contain NO executable programs, and a weekly scan along with the rest of your computer with Thunderbird closed should be more than adequate. Perhaps scheduled for1am Friday. Gives Friday to deal with anything found and does not interrupt your use of the device.
A similar exclusion can also be beneficial for other data storage areas (databases especially)
Finally look at what processes run on your computer. there aerew by default about 40 when it is new and over time this grows with almost every security, office or game you install until your computer is so busy running background processes to check if the latest versions of XXXX has been released that it becomes sluggish and performance on most things is degraded (That common nugget of Windows computers getting slower over time is TRUE, but a large part of that is added processes and security software which is actually reducing performance quite extensively.)
BTW right clicking a folder, selecting properties and the repair button rebuilds the index non destructively as deleting the files as you mention also looses tags.

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