Have you tried with omitting all the default charset and charset directives in my.cnf? Maybe these are causing the trouble. I've been using 5.5, 10.3, 10.5 for many years and never saw a similar issue, but I also never had a specific charset set in my.cnf, so I am guessing that this could have something to do with it.
Hello
I have the same problem, when I upgraded Plesk to 18.56, SQL crashed.
ERROR 1273 (HY000) at line 234: Unknown collation: 'utf8_general_ci'
ERROR 1115 (42000) at line 245: Unknown character set: 'utf8'
ERROR 1273 (HY000) at line 251: Unknown collation: 'utf8_general_ci'
ERROR 1115 (42000) at line 275: Unknown character set: 'utf8'
ERROR 1273 (HY000) at line 280: Unknown collation: 'utf8_general_ci'
ERROR 1115 (42000) at line 293: Unknown character set: 'utf8'
ERROR 1273 (HY000) at line 297: Unknown collation: 'utf8_general_ci'
ERROR 1115 (42000) at line 310: Unknown character set: 'utf8'
ERROR 1273 (HY000) at line 312: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 345: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 351: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 352: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 353: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 354: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 355: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 356: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 357: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 358: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 359: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 360: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 361: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 362: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 366: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 367: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 368: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 369: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 370: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 371: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 372: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 373: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 374: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 375: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 376: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 377: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 378: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 379: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 380: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 381: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 389: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 390: Unknown collation: 'utf8_general_ci'
ERROR 1115 (42000) at line 394: Unknown character set: 'utf8'
ERROR 1273 (HY000) at line 397: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 400: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 403: Unknown collation: 'utf8_general_ci'
ERROR 1115 (42000) at line 408: Unknown character set: 'utf8'
ERROR 1115 (42000) at line 455: Unknown character set: 'utf8'
ERROR 1273 (HY000) at line 459: Unknown collation: 'utf8_bin'
ERROR 1273 (HY000) at line 462: Unknown collation: 'utf8_bin'
ERROR 1273 (HY000) at line 479: Unknown collation: 'utf8_bin'
ERROR 1273 (HY000) at line 482: Unknown collation: 'utf8_bin'
ERROR 1273 (HY000) at line 491: Unknown collation: 'utf8_bin'
ERROR 1273 (HY000) at line 494: Unknown collation: 'utf8_bin'
ERROR 1273 (HY000) at line 509: Unknown collation: 'utf8_bin'
ERROR 1115 (42000) at line 515: Unknown character set: 'utf8'
ERROR 1115 (42000) at line 516: Unknown character set: 'utf8'
ERROR 1115 (42000) at line 518: Unknown character set: 'utf8'
ERROR 1115 (42000) at line 519: Unknown character set: 'utf8'
ERROR 1115 (42000) at line 558: Unknown character set: 'utf8'
ERROR 1273 (HY000) at line 564: Unknown collation: 'utf8_bin'
ERROR 1273 (HY000) at line 567: Unknown collation: 'utf8_bin'
ERROR 1273 (HY000) at line 569: Unknown collation: 'utf8_bin'
ERROR 1273 (HY000) at line 572: Unknown collation: 'utf8_bin'
ERROR 1273 (HY000) at line 574: Unknown collation: 'utf8_bin'
ERROR 1273 (HY000) at line 577: Unknown collation: 'utf8_bin'
ERROR 1408 (HY000) at line 582: Event Scheduler: An error occurred when initializing system tables. Disabling the Event Scheduler.
ERROR 1273 (HY000) at line 585: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 586: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 587: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 588: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 589: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 590: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 594: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 595: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 597: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 598: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 601: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 602: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 603: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 604: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 609: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 610: Unknown collation: 'utf8_general_ci'
ERROR 1273 (HY000) at line 613: Unknown collation: 'utf8_general_ci'
ERROR 1728 (HY000) at line 626: Cannot load from mysql.proc. The table is probably corrupted
ERROR 1728 (HY000) at line 628: Cannot load from mysql.proc. The table is probably corrupted
ERROR 1728 (HY000) at line 636: Cannot load from mysql.proc. The table is probably corrupted
ERROR 1728 (HY000) at line 638: Cannot load from mysql.proc. The table is probably corrupted
ERROR 1273 (HY000) at line 668: Unknown collation: 'utf8_bin'
ERROR 1273 (HY000) at line 669: Unknown collation: 'utf8_bin'
ERROR 1273 (HY000) at line 670: Unknown collation: 'utf8_bin'
ERROR 1273 (HY000) at line 671: Unknown collation: 'utf8_bin'
ERROR 1273 (HY000) at line 672: Unknown collation: 'utf8_bin'
ERROR 1273 (HY000) at line 674: Unknown collation: 'utf8_bin'
ERROR 1273 (HY000) at line 675: Unknown collation: 'utf8_bin'
ERROR 1115 (42000) at line 702: Unknown character set: 'utf8'
ERROR 1243 (HY000) at line 703: Unknown prepared statement handler (stmt) given to EXECUTE
ERROR 1243 (HY000) at line 704: Unknown prepared statement handler (stmt) given to DEALLOCATE PREPARE
FATAL ERROR: Upgrade failed
[root@server ~]#