It's safe to do and actually saves render time compared with rendering each version separately.
If you are rendering to a delivery format such as an MP4 as one of your versions then you should render a production master from the Render Cue and render your delivery product using the Adobe Media Encoder. The output module does not do a very good job of rendering highly compressed formats like MPEG and H.264. You should not use Quciktime H.264 for any of your rendering. It's obsolete, no longer supported by Apple and never worked very well.
I usually render one file out of After Effects and then use a similar workflow to the one you describe in the Adobe Media Encoder to make my deliverables.
After Effects can't do multipass encoding, so if you're making H.264's, as Rick says, you're really going to want a less-buggy more multipass-capable encoder like the Adobe Media Encoder.
you're both right, you CAN do it but it crashed a few times, obviously not the best way, thanks for letting me know
hi Rick, so as I use exclusively the h264 at the moment - because it makes small files - which would you recommend as a replacement codec that also would make small files (compared to the huge Animation codec for instance) thanks
what you render out of AE will be an intermediate codec, so it will be uncompressed (or close to it) and thus rather large. Once you use that file in Adobe Media Encoder to make your deliverable (H.264, in your case), you can get rid of the large intermediate file if you want to.
An an alternative solution would be to send your AE comp directly to the Adobe Media Encoder. Advantages are you don't have to deal with intermediate files and you can send a company to render and then keep working while AME renders in the background. Disadvantages include it's a slower render and if you need to adjust your compression settings, you need to re-render the whole thing again Whereas, if you render an intermediate file and build your deliverable from that, you just redo the compression instead of having to render your whole, complicated comp.
H.264 is a delivery codec not suitable to be re-compressed at a later time. The loss in quality from re-compressing highly compressed footage, even if you increase the data rate can be extreme. I would never use h.264 to archive anything for potential future use. NEVER.
There are several highly compressed MPEG formats that consumer and even semi-pro video cameras use. This codec is meant to be decoded once before it's processed. If you try and re-encode to the same format you loose quality. I don't know why that's so hard for folks to understand. With MPEG (h.264) compression you don't even have complete frames. You'll get a block of color that is a bunch of pixels and some pretty decent although compressed luminance information for one frame, then some frames are skipped and you get another block of colors and some more pretty decent but compressed luminance information, then the encode part of the process makes it's best guess as to where the luminance pixels in the first full frame have moved and what path they took getting to the second frame and it represents only the pixels that moved between frames, then that information is used to calculate where the software thinks the color went and only render those frames. In the decode part of the process full frames are recreated from those calculations. EVERY time that information is re encoded data is lost, color artifacts and motion artifacts increase and you loose image quality.
In a lossless or visually lossless format like GoPro's Cineware, Avid, ProRez and a bunch of other formats every frame is encoded. Professional formats can encode color at 10 bits or higher. These formats also do a better job of compressing or averaging the color samples, some of them have the capability of giving you 4:4:4 color (color info for every pixel) Uncompressed gives you data for every pixel of every frame and the color can be averaged (QuickTime Animation) for example. Visually lossless 8 bit codecs like Quicktime JPEG 2000 and QuickTime PNG even support alpha channels for production purposes. NOTE: no media player on any web browser or computer screen will support alpha channels. Transparency is always shown as black.
You can get a 2 TB hard drive for under $100 - There is no reason to not render a production master for any video you plan use in another production or edit in any way again.
Home movies of the kids or things you are going to send to YouTube or Instagram and forget are another matter. Render one HD 1080p 29.97 or 30 fps copy (24 if you are a glutton for punishment and don't mind pans and motion that judders like crazy once in a while because you did not consider critical panning speeds) and send it to Vimeo or YouTube using their recommended compression settings. If you want to send and forget 4K to the net and the world then study up on the standards for that frame rate and send ONE version of that video to those streaming services using their standards for compression. YouTube, Vimeo and any other streaming service you choose will take your highest resolution copy and render their own lower frame size versions to serve up to the public with their automated services. I can think of no reason to render multiple copies of a delivery format like h.264 unless you have a client that wants a commercial or tv program sent to several different TV stations or cable channels and each of them have a different standard for delivery. If you are working for clients or sending stuff out for broadcast then it is a foolish business decision to not render a visually lossless production master to put in your archives.