Class file repeatedly becomes missing from registry table

Description:
This happens for one of the subsites in multisite Drupal installation.
For this subsite we have a module with following line in the info file:
files[] = plugins/services_entity_extensions_clean/ReservationPlugin.class.php
Obviously Drupal registry table should contain a record for this class, and it initially does:

MariaDB [*database*]> select filename from registry where filename like '%reservation%';
+-----------------------------------------------------------------------------------+
| filename                                                                          |
+-----------------------------------------------------------------------------------+
| sites/*sitename*/modules/site/parts/***_services/plugins/services_entity_extensions_clean/ReservationPlugin.class.php |
+-----------------------------------------------------------------------------------+
1 row in set (0.00 sec)

But after some random time this record keeps disappearing from registry table. And the following PHP code:

new ReservationPlugin();

yields a "Class not found" error.
The only way to get record for this file back into the table is to insert it manually. drush cc and/or drush rr do not help.

Further research showed that even if record is missing from the registry table, it is still present in the registry_file table:

MariaDB [*database*]> select filename from registry_file where filename like '%reservation%';
+-----------------------------------------------------------------------------------+
| filename                                                                          |
+-----------------------------------------------------------------------------------+
| sites/*sitename*/modules/site/parts/***_services/plugins/services_entity_extensions_clean/ReservationPlugin.class.php |
+-----------------------------------------------------------------------------------+
1 row in set (0.01 sec)

Repeatable: Random
Steps to repeat: nothing specific, it just appears from time to time throwing PHP error when class is being instantiated.
Expected Results: record in registry table is always present for this class.
Actual Results: record for given class in registry table is getting removed at random times.

I know that all above sounds really weird, but still this keeps happening over and over.
I'm open to provide any additional info, if needed.