WSUS Content folder not retaining updates

I have been scratching my head now for a while over this issue and anything I do will not solve the problem

The Problem:

WSUS' "WSUSContent" folder is self-deleting updates and reducing the
overall size to <5GB. The original size was over 300GB. Where have the
updates gone? We did not initiate a WSUSContent cleanup nor have we in the past.

Attempts at solving:

WSUSutil /reset.
Reinstall WSUS service from scratch.
Migrated from internal database to remote SQL database.

Further Information:

• The WSUS database is located on a remote SQL server
• WSUSutil reset rebuilt the whole content folder to over 300GB.
• WSUS was active for a period of time (1-2 weeks) and then suddenly stopped working within one day (unfortunately, we don't know when this happened)
• Frequently after this issue occurs, we get the generic 800 code for WSUS missing content:

2015-03-30 14:25:19:174 1184 195c Setup FATAL: GetClientUpdateUrl
failed, err = 0x8024D009
2015-03-30 14:25:19:174 1184 195c Setup Skipping SelfUpdate check
based on the /SKIP directive in wuident
2015-03-30 14:25:19:174 1184 195c Setup SelfUpdate check completed.
SelfUpdate is NOT required.

• There is no scheduled task to "cleanup" the updates and we automatically approve all updates for the required technologies (Windows 7, 8.1, Server 2012, SQL 2012, and others which have eluded me off the top of my head).
• We have used third-party tools to check our WSUS setup and they all return with the claim that the setup is fine and no problems were detected.
• We have WSUS working on HTTP and HTTPS, SSL certificate is fine and within date/valid.
• When connecting with Administrator tools to WSUS, the console periodically will break and display a red "X" and state that the remote API stopped working? (I am pasting below another error which the WSUS administration console experiences):

The WSUS administration console has encountered an unexpected error.
This may be a transient error; try restarting the administration
console. If this error persists,

Try removing the persisted preferences for the console by deleting the
wsus file under %appdata%\Microsoft\MMC.

System.Collections.Generic.KeyNotFoundException — The given key was
not present in the dictionary.

Source mscorlib

Stack Trace: at
System.Collections.Generic.Dictionary`2.get_Item(TKey key) at
Microsoft.UpdateServices.UI.SnapIn.Pages.UpdatesListPage.GetUpdateRow(WsusUpdate
update) at
Microsoft.UpdateServices.UI.SnapIn.Pages.UpdatesListPage.GetListRows()

• I have followed these on SF, to no luck:

WSUS not receiving updates?
&
WSUS, installed, not applicable

Many others on the internet also to try and find an answer.

• The WSUS server is part of a domain and to clarify, when I ran wsusutil /reset, all clients connected were getting updates and connectivity is not an issue, WSUS content just disappears with no trace.

Windows Log File "Red" Entries:

These are the critical log entries I have tried looking into, to no avail also, unless I am overlooking something..

• 376 1b0c Misc WARNING: Network Cost is assumed to be not supported as something failed with trying to get handles to wcmapi.dll
• Report WARNING: Reporter failed to upload events with hr = 8007000d.
• WARNING: Failed converting event batch to web service event: 0x8007000d
• FATAL: GetClientUpdateUrl failed, err = 0x8024D009
• WARNING: Failed to get Wu Exemption info from NLM, assuming not exempt, error = 0x80240037
• Agent * Online = No; Ignore download priority = No <- Online = No; ???

Any help would be appreciated as this is just very unusual to happen.