I tried shutting down XAMPP and deleting the ibdata1 already. Yesterday the server did still work, but when starting up today it didn't start anymore. I'm using the server for a PHP project using PHPMyAdmin. This is the error log from XAMPP:
2016-05-26 09:07:29 15a0 InnoDB: Warning: Using innodb_additional_mem_pool_size is DEPRECATED.
This option may be removed in future releases, together with the option innodb_use_sys_malloc and with the InnoDB's internal memory allocator.
160526 9:07:29 [Note] InnoDB: Using mutexes to ref count buffer pool pages
160526 9:07:29 [Note] InnoDB: The InnoDB memory heap is disabled
160526 9:07:29 [Note] InnoDB: Mutexes and rw_locks use Windows interlocked functions
160526 9:07:29 [Note] InnoDB: Memory barrier is not used
160526 9:07:29 [Note] InnoDB: Compressed tables use zlib 1.2.3
160526 9:07:29 [Note] InnoDB: Not using CPU crc32 instructions
160526 9:07:29 [Note] InnoDB: Initializing buffer pool, size = 16.0M
160526 9:07:29 [Note] InnoDB: Completed initialization of buffer pool
160526 9:07:29 [Note] InnoDB: Restoring page 0 of tablespace 0
160526 9:07:29 [Warning] InnoDB: Doublewrite does not have page_no=0 of space: 0
160526 9:07:29 [ERROR] InnoDB: space header page consists of zero bytes in data file C:\xampp\mysql\data\ibdata1
160526 9:07:29 [ERROR] InnoDB: Could not open or create the system tablespace.
If you tried to add new data files to the system tablespace, and it failed here, you should now edit innodb_data_file_path in my.cnf back to what it was, and remove the new ibdata files InnoDB created in this failed attempt.
InnoDB only wrote those files full of zeros, but did not yet use them in any way.
But be careful: do not remove old data files which contain your precious data!
160526 9:07:29 [ERROR] Plugin 'InnoDB' init function returned error.
160526 9:07:29 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
160526 9:07:29 [Note] Plugin 'FEEDBACK' is disabled.
160526 9:07:29 [ERROR] Unknown/unsupported storage engine: InnoDB
160526 9:07:29 [ERROR] Aborting
160526 9:07:29 [Note] c:\xampp\mysql\bin\mysqld.exe: Shutdown complete`
