I was looking for the answer to the same problem and just used this to 
batch convert everything in my library to Opus alongside my FLAC.

https://github.com/wisp3rwind/beets-alternatives

It seems pretty flexible and can update incrementally

On Friday, May 12, 2017 at 5:57:44 AM UTC-7, Andy Pastuszak wrote:
>
> Then I will need to continue to manually convert.  Now I just need to find 
> a way to compare the two folders and figure out what I haven't converted 
> yet.
>
> On Fri, May 12, 2017 at 8:55 AM, Adrian Sampson <[email protected] 
> <javascript:>> wrote:
>
>> Yep, that is indeed what it does—I don't believe there's an option to do 
>> the other thing (convert to a file on the side) automatically on import.
>>
>> On May 12, 2017, at 8:53 AM, Andy Pastuszak <[email protected] 
>> <javascript:>> wrote:
>>
>> The documentation for the convert plugin makes it sound like it's going 
>> to take your FLAC, convert them to MP3 and then add the MP3 to your 
>> library.  I'm more than willing to give this a try.  Let me go test.
>>
>> On Fri, May 12, 2017 at 8:48 AM, Adrian Sampson <[email protected] 
>> <javascript:>> wrote:
>>
>>> Hi there!
>>>
>>>
>>>
>>> Adrian
>>> > On May 11, 2017, at 10:21 PM, Andy Pastuszak <[email protected] 
>>> <javascript:>> wrote:
>>> >
>>> > If there a way to import my lossless files and then have beets 
>>> automatically run a convert on the files I just imported without me needing 
>>> to manually run convert after the import?
>>>
>>> Have you tried the "auto" configuration option for the concert plugin?
>>>
>>> > Also is there any way to run a convert and have it not convert if 
>>> there is any lossy file at the destination?  So, I am going to convert to 
>>> MP3, I'd like it to see that I already have m4a files in the destination 
>>> and skip converting those files.
>>>
>>> We don't have anything exactly like that.
>>>
>>> > And, lastly....
>>> >
>>> > I run beets on an Ubuntu Linux 16.04 server that I ssh into.  Once the 
>>> convert command completes, I cannot see anything I type.  I usually end up 
>>> killing the SSH session and logging back in.  This the only beets command 
>>> that causes this behavior.  Has anyone else seen this?
>>>
>>> This has recently been fixed in master; we'll include it in a release 
>>> soon. (A judicious GitHub issues search should turn something up.)
>>>
>>> Adrian
>>>
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