After updating to the latest release, 2.2, I've found the FLAC files are no longer deleted after conversion.
22-12-5 17:23:17.5|[8930]Info|Lidarr event: AlbumDownload, Artist: Eric Johnson (881), Album: EJ (20072), Advanced options: '-vn -c:a libopus -b:a 128k', File extension: .opus, Matching regex: '\.(flac|wav)$', Track(s): /music/Eric Johnson/EJ/01-01 Mrs. Robinson.flac|/music/Eric Johnson/EJ/01-02 Water Under the Bridge.flac|/music/Eric Johnson/EJ/01-03 Wonder.flac|/music/Eric Johnson/EJ/01-04 Wrapped in a Cloud.flac|/music/Eric Johnson/EJ/01-05 Once Upon a Time in Texas.flac|/music/Eric Johnson/EJ/01-06 One Rainy Wish.flac|/music/Eric Johnson/EJ/01-07 Serinidad.flac|/music/Eric Johnson/EJ/01-08 Fatherly Downs.flac|/music/Eric Johnson/EJ/01-09 The World Is Waiting for the Sunrise.flac|/music/Eric Johnson/EJ/01-10 November.flac|/music/Eric Johnson/EJ/01-11 All Things You Are.flac|/music/Eric Johnson/EJ/01-12 Scarborough Fair+Canticle.flac|/music/Eric Johnson/EJ/01-13 Song for Irene.flac
22-12-5 17:23:17.6|[8930]Info|Writing: /music/Eric Johnson/EJ/01-01 Mrs. Robinson.opus
22-12-5 17:23:25.2|[8930]Error|Exit code 1 setting permissions and/or recycling on "/music/Eric Johnson/EJ/01-01 Mrs. Robinson.opus"
22-12-5 17:23:25.2|[8930]Info|Writing: /music/Eric Johnson/EJ/01-02 Water Under the Bridge.opus
22-12-5 17:23:30.1|[8930]Error|Exit code 1 setting permissions and/or recycling on "/music/Eric Johnson/EJ/01-02 Water Under the Bridge.opus"
22-12-5 17:23:30.1|[8930]Info|Writing: /music/Eric Johnson/EJ/01-03 Wonder.opus
22-12-5 17:23:36.0|[8930]Error|Exit code 1 setting permissions and/or recycling on "/music/Eric Johnson/EJ/01-03 Wonder.opus"
22-12-5 17:23:36.0|[8930]Info|Writing: /music/Eric Johnson/EJ/01-04 Wrapped in a Cloud.opus
22-12-5 17:23:46.0|[8930]Error|Exit code 1 setting permissions and/or recycling on "/music/Eric Johnson/EJ/01-04 Wrapped in a Cloud.opus"
22-12-5 17:23:46.0|[8930]Info|Writing: /music/Eric Johnson/EJ/01-05 Once Upon a Time in Texas.opus
22-12-5 17:23:52.3|[8930]Error|Exit code 1 setting permissions and/or recycling on "/music/Eric Johnson/EJ/01-05 Once Upon a Time in Texas.opus"
22-12-5 17:23:52.3|[8930]Info|Writing: /music/Eric Johnson/EJ/01-06 One Rainy Wish.opus
22-12-5 17:24:00.1|[8930]Error|Exit code 1 setting permissions and/or recycling on "/music/Eric Johnson/EJ/01-06 One Rainy Wish.opus"
22-12-5 17:24:00.1|[8930]Info|Writing: /music/Eric Johnson/EJ/01-07 Serinidad.opus
22-12-5 17:24:04.3|[8930]Error|Exit code 1 setting permissions and/or recycling on "/music/Eric Johnson/EJ/01-07 Serinidad.opus"
22-12-5 17:24:04.3|[8930]Info|Writing: /music/Eric Johnson/EJ/01-08 Fatherly Downs.opus
22-12-5 17:24:11.3|[8930]Error|Exit code 1 setting permissions and/or recycling on "/music/Eric Johnson/EJ/01-08 Fatherly Downs.opus"
22-12-5 17:24:11.3|[8930]Info|Writing: /music/Eric Johnson/EJ/01-09 The World Is Waiting for the Sunrise.opus
22-12-5 17:24:16.3|[8930]Error|Exit code 1 setting permissions and/or recycling on "/music/Eric Johnson/EJ/01-09 The World Is Waiting for the Sunrise.opus"
22-12-5 17:24:16.3|[8930]Info|Writing: /music/Eric Johnson/EJ/01-10 November.opus
22-12-5 17:24:26.4|[8930]Error|Exit code 1 setting permissions and/or recycling on "/music/Eric Johnson/EJ/01-10 November.opus"
22-12-5 17:24:26.5|[8930]Info|Writing: /music/Eric Johnson/EJ/01-11 All Things You Are.opus
22-12-5 17:24:35.1|[8930]Error|Exit code 1 setting permissions and/or recycling on "/music/Eric Johnson/EJ/01-11 All Things You Are.opus"
22-12-5 17:24:35.1|[8930]Info|Writing: /music/Eric Johnson/EJ/01-12 Scarborough Fair+Canticle.opus
22-12-5 17:24:43.3|[8930]Error|Exit code 1 setting permissions and/or recycling on "/music/Eric Johnson/EJ/01-12 Scarborough Fair+Canticle.opus"
22-12-5 17:24:43.4|[8930]Info|Writing: /music/Eric Johnson/EJ/01-13 Song for Irene.opus
22-12-5 17:24:48.9|[8930]Error|Exit code 1 setting permissions and/or recycling on "/music/Eric Johnson/EJ/01-13 Song for Irene.opus"
22-12-5 17:24:48.9|[8930]Info|Calling Lidarr API to rescan artist
22-12-5 17:25:03.8|[8930]Info|Completed in 1m 48s
And here's the output for the next album, using 2.1 by pinning it with the Docker Hub tag:
22-12-5 18:06:16.7|[310]Info|Lidarr event: AlbumDownload, Artist: Eric Johnson (881), Album: The Book of Making (20070), Advanced options: '-vn -c:a libopus -b:a 128k', File extension: .opus, Matching regex: '\.(flac|wav)$', Track(s): /music/Eric Johnson/The Book of Making/01-01 Soundtrack Life.flac|/music/Eric Johnson/The Book of Making/01-02 Floating Through This World.flac|/music/Eric Johnson/The Book of Making/01-03 Love Will Never Say Goodbye.flac|/music/Eric Johnson/The Book of Making/01-04 Bigger Than My Life.flac|/music/Eric Johnson/The Book of Making/01-05 Just To Be With You.flac|/music/Eric Johnson/The Book of Making/01-06 To Be Alive.flac|/music/Eric Johnson/The Book of Making/01-07 Another One Like You.flac|/music/Eric Johnson/The Book of Making/01-08 My Faith In You.flac|/music/Eric Johnson/The Book of Making/01-09 A Thousand Miles.flac
22-12-5 18:06:16.8|[310]Info|Writing: /music/Eric Johnson/The Book of Making/01-01 Soundtrack Life.opus
22-12-5 18:06:24.3|[310]Info|Writing: /music/Eric Johnson/The Book of Making/01-02 Floating Through This World.opus
22-12-5 18:06:29.3|[310]Info|Writing: /music/Eric Johnson/The Book of Making/01-03 Love Will Never Say Goodbye.opus
22-12-5 18:06:36.3|[310]Info|Writing: /music/Eric Johnson/The Book of Making/01-04 Bigger Than My Life.opus
22-12-5 18:06:40.6|[310]Info|Writing: /music/Eric Johnson/The Book of Making/01-05 Just To Be With You.opus
22-12-5 18:06:45.8|[310]Info|Writing: /music/Eric Johnson/The Book of Making/01-06 To Be Alive.opus
22-12-5 18:06:53.8|[310]Info|Writing: /music/Eric Johnson/The Book of Making/01-07 Another One Like You.opus
22-12-5 18:07:00.8|[310]Info|Writing: /music/Eric Johnson/The Book of Making/01-08 My Faith In You.opus
22-12-5 18:07:07.7|[310]Info|Writing: /music/Eric Johnson/The Book of Making/01-09 A Thousand Miles.opus
22-12-5 18:07:11.6|[310]Info|Calling Lidarr API to rescan artist
22-12-5 18:07:26.3|[310]Info|Completed in 1m 11s