When your partner is applying for a partner-sponsored temporary work visa, he will have to prove that you have lived together with him steadily
week by week for around two to three months up to the time of submitting the application (and then on through the time of processing). Here
https://www.google.co.uk/#q=site:enz...tnership+proof are old threads with discussion of partnership applications and examples of what people have used. Any gaps in the recent record of proof will be looked at by INZ and you will be asked for explanations why you were not together then, and proof of how you kept in touch and kept up your relationship. INZ are inclined to interpret time spent apart as signalling a possible break-down in the relationship.
So yes, going on holiday on your own will have the effect of causing you more effort to prove your situation. Even going BEFORE you apply will potentially be a nuisance to you in the long run.